Information on EC 3.1.27.5 - pancreatic ribonuclease

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY
3.1.27.5
-
RECOMMENDED NAME
GeneOntology No.
pancreatic ribonuclease
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
-
-
-
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
the catalytic site of the enzyme is mainly composed of His12, His119, Gln11, Lys41 and Asp121. The conformation of Lys41 and Gln11 are pH dependent and their occurrence is correlated to the release of a sulfate ion from the active site at neutral pH. The sulfate anion is progressively released with pH and water molecules occupy the active site at pH 7.1. The enzyme adopts different conformational states in different pH conditions. In the protonated state, Lys41 points towards the active site both in the presence and in the absence of sulfate and acts as a general base during catalysis
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
Gly38 and Glu111 are crucial for the catalytic activity
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
specifically located basic residues, together with the lack of a negative charge and/or the presence of a glycine at position 38, may contribute to make the enzymatic degradation of the polyanionic double-helical substrate more efficient
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
two isoforms of dimeric enzyme, D-I and D-II
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
protein with 124 amino acid residues and four intra-molecular disulfide bonds. In the presence of oxidized and reduced dithiothreitol at pH 8.0 and 25C, the enzyme folds through pathways involving a rapid pre-equilibrium resulting in an ensemble of three-disulfide intermediate species. Protein disulfide isomerase catalyzes the conversion of the intermediates to the native enzyme, by acting as both a chaperone and an oxidase on the on-pathway intermediate
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
the enzyme is composed of 124 amino acid residues. The amino acid residues involved in catalysis are His12, His119 and Lys41. The enzyme has six substrate binding subsites. One of them, B1, binds only to pyrimidine nucleotides and prefers to bind cytidine rather than uridine. Thr45 of the B1 subsite contributes to the enzyme substrate specificity and plays an important role in catalysis. Phe120 in the B1 subsite enhances substrate binding with the aid of its pi electron and hydrophobicity. Asn71 in the B2 subsite is responsible for productive interactions leading to efficient activity, and Glu111 in the same subsite contributes to substrate binding only in the binding of guanosine. Lys7, Arg10 and Gln11 in the P2 subsite also play an important role in catalysis. Some amino acid residues are located in the vicinity of the catalytic residues and contribute to the catalytic reaction by interacting with catalytic residues. Lys7, Arg10 and Lys66 maintain the optimum pKa of His12 and His119. Asp121 positions the proper tautomer of His119. Phe120 is responsible for the strict positioning of His119, and contributes to conformational stability. Tyr97 is involved in maintaining the correct position of Lys41. Cys65-Cys72 are located close to the catalytic and substrate binding residues and contribute to the proper spatial alignment of these residues
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
pyrimidine-specific endoribonuclease which cleaves 3',5'-phosphodiester bonds of single strand RNA via transphosphorylation and subsequent hydrolysis reactions
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
protein of 128 amino acid residues, catalyses the cleavage of RNA specifically on the 3'-side of pyrimidine bases. The catalytic triad comprises His12, Lys41 and His119. The amino acid sequence of the enzyme is longer than that of its bovine counterpart, with four extra amino acid residues at the C-terminal region
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
sequential binding of the monomeric substrate in a concentration-dependent manner makes up the active site of the enzyme
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
His12, His119 and Lys41 comprise the catalytic site, and several other amino acid residues serve as substrate binding subsites. The mutagenic replacement of Phe120 causes a positional change in His119 and that is a major cause in decreasing the activity of the enzyme. Phe120 is important in fixing the proper spatial position of His119 near the C-terminal region for efficient activity. Phe120 interacts not directly with His119, but with the hydrophobic core
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
His119 and His12 play an important structural role in active site of RNase A
-
endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates
show the reaction diagram
enzymatic reaction mechanism, analysis of different versions, e.g. mechanism of Mathias and Rabin for catalysis of the hydrolysis of cytidine 2',3'-cyclic phosphate by RNase A, overview. Model of the RNase A-substrate complex, subsites of RNase A. Bn, Rn, and Rho_n are nucleobase-, ribose-, and phosphate-binding subsites, respectively
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
alkaline ribonuclease
-
-
-
-
alkaline ribonuclease
-
-
bovine pancreatic ribonuclease A
P61823
-
BS-RNase
-
-
BS-RNase
P00669
-
Ceratitis capitata alkaline ribonuclease
-
-
-
-
EC 2.7.7.16
-
-
formerly
-
EC 3.1.4.22
-
-
formerly
-
EC-RNase
-
-
Eosinophil-derived neurotoxin
-
-
-
-
gene S glycoproteins
-
-
-
-
gene S locus-specific glycoproteins
-
-
-
-
glycoproteins, gene S locus-specific
-
-
-
-
glycoproteins, S-genotype-asssocd
-
-
-
-
glycoproteins, SLSG
-
-
-
-
glycoproteins, specific or class, gene S
-
-
-
-
glycoproteins, specific or class, SLSG (gene S locus-specific glycoprotein)
-
-
-
-
HP-RNase
-
-
nuclease, ribo-
-
-
-
-
onconase
-
-
pancreatic ribonuclease
-
-
pancreatic ribonuclease
C9DEB3, C9DEB5
-
pancreatic ribonuclease
C9DEB2, C9DEB4
-
pancreatic ribonuclease
-
-
pancreatic ribonuclease
-
R67L, K130N, single nucleotide polymorphisms
pancreatic ribonuclease
P14626
-
pancreatic ribonuclease
C9DEA9, C9DEB0
-
pancreatic ribonuclease
C9DEA8, C9DEB1
-
pancreatic ribonuclease
C9DEC7, C9DEC8
-
pancreatic ribonuclease
C9DEC5, C9DEC6
-
pancreatic ribonuclease
C9DEB8, C9DEC2
-
pancreatic ribonuclease
C9DEB7, C9DEC4
-
pancreatic ribonuclease
C9DEB6, C9DEC3
-
pancreatic ribonuclease
C9DEB9, C9DEC0, C9DEC1
-
pancreatic ribonuclease A
-
-
pancreatic ribonuclease A
P61823
-
pancreatic RNase
-
-
-
-
pancreatic RNase
-
-
ribonuclease
-
-
-
-
ribonuclease A
-
-
-
-
ribonuclease A
P14626
-
ribonuclease I
-
-
-
-
ribonuclease I
P21338
-
Ribonuclease US
-
-
-
-
ribonuclease W1
-
-
-
-
ribonucleate 3'-pyrimidino-oligonucleotidohydrolase
-
-
-
-
ribonucleic phosphatase
-
-
-
-
RL1
-
-
-
-
RNase
-
-
-
-
RNase A
-
-
-
-
RNase I
-
-
-
-
RNase-A
-
-
RNase1
-
-
RNase1
-
-
RNase9
Q5QJV3
-
RnaseA
-
-
S-RNase
-
-
-
-
seminal ribonuclease
-
-
seminal ribonuclease
P00669
-
Seminal RNase
-
-
-
-
SLSG glycoproteins
-
-
-
-
type I RNase A
-
isoform with the same molecular mass as that of a commercial RNase A
type II RNase A
-
isoform with higher molecular mass than commercial and type I RNase A
additional information
-
the enzyme is a member of RNase A superfamily
CAS REGISTRY NUMBER
COMMENTARY
9001-99-4
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
commercial preparation
-
-
Manually annotated by BRENDA team
commercial preparation
Swissprot
Manually annotated by BRENDA team
commercial product
-
-
Manually annotated by BRENDA team
expression in Nicotiana tabacum as a protection against tobacco mosaic virus
Swissprot
Manually annotated by BRENDA team
mutant
-
-
Manually annotated by BRENDA team
Type XII A, commercial product, Sigma
-
-
Manually annotated by BRENDA team
Type XII-A, commercial preparation
-
-
Manually annotated by BRENDA team
Cervus capreolus
red deer
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
topi, 2 forms: A and B differ in carbohydrate
-
-
Manually annotated by BRENDA team
isoform RNase1
SwissProt
Manually annotated by BRENDA team
isoform RNase2
-
-
Manually annotated by BRENDA team
isoform RNase3, expressed in 5 day old fish
SwissProt
Manually annotated by BRENDA team
isoform RNase A-1
SwissProt
Manually annotated by BRENDA team
isoform RNase A-2
SwissProt
Manually annotated by BRENDA team
; comparison of pancreatic ribonuclease and ribonuclease A
Uniprot
Manually annotated by BRENDA team
3 forms: A, B, C: same amino acid composition, B and C: glycoproteins, A: not
-
-
Manually annotated by BRENDA team
bullfrog
SwissProt
Manually annotated by BRENDA team
frog, mutant
-
-
Manually annotated by BRENDA team
isoform RNase9
SwissProt
Manually annotated by BRENDA team
enzyme exhibits RNase activity as well as DNA-binding properties
-
-
Manually annotated by BRENDA team
ribonuclease activity of Sso7d DNA-binding protein
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
-
mechanistic model for the denaturation of bovine pancreatic ribonuclease A in urea, a direct interaction between urea and protonated histidine as the initial step for protein inactivation followed by hydrogen bond formation with polar residues, and the breaking of hydrophobic collapse as the final steps for protein denaturation
physiological function
-
His12 acts mainly as a general base in the catalytic process of RNase A
malfunction
-
RNase A tandem enzymes, in which two RNase A molecules are artificially connected by a peptide linker, and thus have a pseudodimeric structure, exhibit remarkable cytotoxic activity, but can be inhibited by the cytosolic ribonuclease inhibitor in vitro. Structure modeling, overview
additional information
-
analysis of the disulfide bond formation phase in detail in the oxidative folding, as the first of two folding phases, of RNase A, overview. Comparision of folding intermediates of reduced RNase A obtained at 25C and different pH values from pH 4.0, pH 7.0, to pH 10.0, shuffling and transformation of different intermediate types, overview. The preconformational folding phase coupled with disulfide bond formation can be divided into two distinct subphases, a kinetic (or stochastic) disulfide bond formation phase and a thermodynamic disulfide bond reshuffling phase. The transition from kinetically formed to thermodynamically stabilized disulfide bond intermediates are induced by hydrophobic nucleation as well as generation of the native interactions
additional information
-
analysis of synthesis and maturation, folding, quality control, and secretion, of pancreatic RNase in the endoplasmic reticulum of live cells, overview. In contrast to the slow in vitro refolding, the protein folds almost instantly after translation and translocation into the endoplasmatic reticulum lumen. Despite high stability of the native protein, only about half of the RNase reaches a secretion competent, monomeric form and is rapidly transported from the rough endoplasmic reticulum via the Golgi complex to the extracellular space
additional information
-
analysis of synthesis and maturation, folding, quality control, and secretion, of pancreatic RNase in the endoplasmic reticulum of live cells, overview. Human RNase folds rapidly and is secreted mainly in glycosylated forms
additional information
-
domain swapping, the process in which a structural unit is exchanged between monomers to create a dimer containing two versions of the monomeric fold, is believed to be an important mechanism for oligomerization and the formation of amyloid fibrils. In RNase residue P114 acts as a conformational gatekeeper, regulating interconversion between monomer and domain-swapped dimer forms, with cis and trans conformation, isomerization at P114 may facilitate population of a partially unfolded intermediate or alternative structure competent for domain swapping, overview
additional information
-
arginine 39 is crucial for the dsRNA melting activity, and Gly38 is required, both these residues are not directly involved in the RNA cleavage activity
additional information
-
pancreatic ribonuclease A shows domain swapping, a type of oligomerization in which monomeric proteins exchange a structural element, resulting in oligomers whose subunits recapitulate the native, monomeric fold, under extreme conditions, such as lyophilization from acetic acid. The major domain swaps dimer form of RNase A exchanges a beta-strand at its C-terminus to form a C-terminal domain-swapped dimer, mechanism, overview. Domain swapping occurs via a local high-energy fluctuation at the C-terminus
additional information
-
very subtle structural, chemical, and potentially motional variations contribute to ligand discrimination in the enzyme
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
18S rRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
2',3'-cCMP + H2O
?
show the reaction diagram
-
-
-
-
?
2',3'-cCMP + H2O
3'-CMP
show the reaction diagram
-
-
-
-
?
28S rRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
5S rRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine + H2O
?
show the reaction diagram
-
-
-
-
?
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine + H2O
?
show the reaction diagram
-
-
-
-
?
6-carboxyfluorescein-dArUdGdA-6-carboxytetramethylrhodamine + H2O
?
show the reaction diagram
-
-
-
-
?
benzyl uridine + H2O
benzyl alcohol + 3'-UMP
show the reaction diagram
-
of uridine or cytidine
-
-
?
CpA + H2O
adenosine + 3'-CMP
show the reaction diagram
-
-
-
-
-
CpA + H2O
adenosine + 3'-CMP
show the reaction diagram
-
-
-
-
?
CpA + H2O
adenosine + 3'-CMP
show the reaction diagram
-
-
-
-
?
CpG + H2O
guanosine + 3'-CMP
show the reaction diagram
-
-
-
-
?
cyclic 2',3'-cytidine monophosphate + H2O
3'-CMP
show the reaction diagram
P07998
-
-
-
?
cyclic 2',3'-cytidine monophosphate + H2O
3'-CMP
show the reaction diagram
-
-
-
-
ir
cyclic 2',3'-cytidine monophosphate + H2O
3'-CMP
show the reaction diagram
P61823
-
-
-
?
cyclic 2',3'-cytidine monophosphate + H2O
3'-CMP
show the reaction diagram
-
-
-
-
?
cyclic 2',3'-cytidine monophosphate + H2O
3'-CMP
show the reaction diagram
-
-
-
-
ir
cyclic 2',3'-cytidine monophosphate + H2O
3'-CMP
show the reaction diagram
-
-
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
-
-
-
?
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
Cervus capreolus, Capreolus capreolus
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-nucleoside monophosphate + H2O
3'-phosphomononucleotides
show the reaction diagram
-
second step of hydrolysis is irreversible
-
-
ir
cyclic 2',3'-uridine monophosphate + H2O
3'-UMP
show the reaction diagram
-
-
-
-
ir
cytidine 2',3'-cyclic monophosphate + H2O
cytidine 3'-phosphate
show the reaction diagram
-
-
-
-
?
cytidine-2',3'-cyclic monophosphate + H2O
3'-CMP
show the reaction diagram
-
-
-
-
?
cytidine-2',3'-cyclic monophosphate + H2O
3'-CMP
show the reaction diagram
-
hydrolysis reaction
-
-
?
cytidine-2',3'-cyclic monophosphate + H2O
3'-CMP
show the reaction diagram
P61823
hydrolysis reaction
-
-
?
cytidine-2',3'-cyclic monophosphate + H2O
3'-CMP
show the reaction diagram
-
hydrolysis reaction
-
-
?
cytidinyl-3',5'-adenosine + H2O
adenosine + 3'-CMP
show the reaction diagram
-
CpA
-
-
?
cytidinyl-3',5'-adenosine + H2O
adenosine + 3'-CMP
show the reaction diagram
-
CpA, transphosphorylation reaction
-
-
?
DNA-RNA hybrids + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
in seminal plasma
-
-
?
double-stranded poly(A)-poly(U) + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
-
-
-
-
?
double-stranded RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
in seminal plasma
-
-
?
double-stranded RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
dsRNA
-
-
?
pentacytidylic acid + H2O
?
show the reaction diagram
-
-
-
-
?
poly (C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
poly (C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
poly (C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
poly (C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
poly (C) + H2O
3'-CMP + 3'-phospho-oligo(C)
show the reaction diagram
P07998
-
-
-
?
poly U + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
-
-
-
-
?
poly U + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
-
-
-
-
?
poly U + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
-
-
-
-
?
poly U + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
-
liver enzyme, low activity
-
-
?
poly(A) + H2O
3'-AMP + 3'-oligonucleotides
show the reaction diagram
-
-
-
-
?
poly(A) + H2O
3'-AMP + 3'-oligonucleotides
show the reaction diagram
P07998
poor substrate because of Thr45 in the substrate binding site of the enzyme that sterically excludes purine bases
-
-
?
poly(A)-poly(U) + H2O
?
show the reaction diagram
-
-
-
-
?
poly(A)-poly(U) + H2O
?
show the reaction diagram
-
the enzyme dimers degrade poly(A)-poly(U) dsRNA with an activity that increases with the increase of the oligomer's basicity
-
-
?
poly(A)poly(U) + H2O
?
show the reaction diagram
P07998
-
-
-
?
poly(A)poly(U) + H2O
?
show the reaction diagram
-
-
-
-
?
poly(A)poly(U)+ H2O
?
show the reaction diagram
-
-
-
-
?
poly(C) + H2O
?
show the reaction diagram
-
-
-
-
?
poly(C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
P07998
-
-
-
?
poly(C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
poly(C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
poly(C) + H2O
3'-CMP + 3'-phosphooligonucleotides
show the reaction diagram
-
35 times more active than with poly(U)
-
-
?
poly(C) + H2O
3'-CMP + 3'-phospho-oligo(C)
show the reaction diagram
-
-
-
-
?
poly(I)poly(C) + H2O
?
show the reaction diagram
-
-
-
-
?
poly(U) + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
-
-
-
-
?
poly(U) + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
P07998
-
-
-
?
poly(U) + H2O
3'-UMP + 3'-oligonucleotides
show the reaction diagram
-
-
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
P14626
-
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
not: single-stranded homopolyribonucleotides other than poly(C) and poly(U)
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
Cervus capreolus, Capreolus capreolus
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
specific for pyrimidine bases
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
high-molecular-weight yeast RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
wheat germ RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
yeast RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
yeast RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
activity against double-stranded RNA and the antitumour action increase with the size of the oligomer
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
enzyme attacks both predicted double- and single-stranded RNA stretches, with no evident preference for specific sequences or individual bases
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
P14626
studies on application to the purification of ribonuclease of Rana catesbeiana eggs using an aqueous-aqueous polymer phase system and a small-scale cross-axis coil planet centrifuge
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
studies on radical scavenging activities of the ribonuclease inhibitor CPRI, a scavenger of pancreatic-type ribonucleases
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
substrate yeast RNA
-
-
?
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
Cervus capreolus, Capreolus capreolus
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
cyclic 2',3'-nucleoside monophosphate
show the reaction diagram
-
first step of hydrolysis is reversible
-
-
r
RNA + H2O
?
show the reaction diagram
-
-
-
-
?
single-stranded RNA + H2O
?
show the reaction diagram
P07998
-
-
-
?
tRNA + H2O
?
show the reaction diagram
Q27J90, Q27J91
substrate yeast tRNA
-
-
?
tRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
tRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
A5HAK0, A5HAK2, -
-
-
-
?
tRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
alkaline RNase, similar enzyme
-
-
?
tRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
onconase, similar enzyme
-
-
?
tRNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
tRNA from yeast
-
-
?
tRNAlys + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
tRNAMet + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
tRNAPhe + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
tRNAVal + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
UpA + H2O
adenosine + 3'-UMP
show the reaction diagram
-
-
-
-
?
UpG + H2O
guanosine + 3'-UMP
show the reaction diagram
-
-
-
-
?
UpG + H2O
guanosine + 3'-UMP
show the reaction diagram
-
-
-
-
?
UpU + H2O
3'-UMP + uridine
show the reaction diagram
-
-
-
-
?
double-stranded RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
P07998
yeast dsRNA
-
-
?
additional information
?
-
-
the four extra amino acid residues in the C-terminal region of the enzyme are proposed to be responsible for a decrease in the ability to cleave poly(C)
-
-
-
additional information
?
-
-
enzyme expressed in K-562 cell is cytotoxic and cytostatic, IC50 value 0.0009 mM
-
-
-
additional information
?
-
Q27J90, Q27J91
enzyme is both angiogenic and bactericidal. Domains II, amino acids 71-76, and III, amino acids 89-104, of RNase A-2 are both important for bactericidal activity
-
-
-
additional information
?
-
A5HAK0, A5HAK2, -
isoform RNase1 is bactericidal with potent activities against the gramnegative bacteria Escherichia coli and Pseudomonas aeruginosa but only mild effects against the gram-positive bacteria Staphylococcus aureus
-
-
-
additional information
?
-
A5HAK0, A5HAK2, -
isoform RNase2 is bactericidal with potent activities against the gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa but only mild effects against the gram-positive bacteria Staphylococcus aureus
-
-
-
additional information
?
-
A5HAK0, A5HAK2, -
isoform RNase3 is bactericidal with potent activities against the gramnegative bacteria Escherichia coli and Pseudomonas aeruginosa but only mild effects against the gram-positive bacteria Staphylococcus aureus
-
-
-
additional information
?
-
-
enzyme is pyrimidine-specific and also acts on 2'-OH modified residues
-
-
-
additional information
?
-
P07998
pancreatic ribonuclease does not act randomly and shows a more endonucleolytic pattern when compared with ribonuclease A. Pancreatic ribonuclease prefers the binding and cleavage of longer substrate molecules with the phosphodiester bond that is broken 8-11 nucleotides away from at least one of the ends of substrate
-
-
-
additional information
?
-
-
predominant cleavage sites for onconase are at UG and GG residues. With the tRNA substrates studied, the predominant cleavages mapin the triplet UGG located in the context of the variable loop or the D-arm of the tRNA
-
-
-
additional information
?
-
-
removal of RNA changes the structural stability of low mobility group nonhistone protein (LMG160), in the way that the molecule tends to become self-associated
-
-
-
additional information
?
-
-
6-carboxyfluorescein-dArU(dA)2-6-carboxytetramethylrhodamine as artificial substrate
-
-
-
additional information
?
-
-
the enzyme shows high activity on double stranded RNA
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
P14626
-
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
Cervus capreolus, Capreolus capreolus
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
RNA + H2O
3'-phosphomononucleotides + 3'-phosphooligonucleotides
show the reaction diagram
-
endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in Cp or Up with 2',3'-cyclic phosphate intermediates, e.g. tRNA, 18S and 28S rRNA, yeast RNA,4.5S RNA
-
-
?
additional information
?
-
-
enzyme expressed in K-562 cell is cytotoxic and cytostatic, IC50 value 0.0009 mM
-
-
-
additional information
?
-
Q27J90, Q27J91
enzyme is both angiogenic and bactericidal. Domains II, amino acids 71-76, and III, amino acids 89-104, of RNase A-2 are both important for bactericidal activity
-
-
-
additional information
?
-
A5HAK0, A5HAK2, -
isoform RNase1 is bactericidal with potent activities against the gramnegative bacteria Escherichia coli and Pseudomonas aeruginosa but only mild effects against the gram-positive bacteria Staphylococcus aureus
-
-
-
additional information
?
-
A5HAK0, A5HAK2, -
isoform RNase2 is bactericidal with potent activities against the gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa but only mild effects against the gram-positive bacteria Staphylococcus aureus
-
-
-
additional information
?
-
A5HAK0, A5HAK2, -
isoform RNase3 is bactericidal with potent activities against the gramnegative bacteria Escherichia coli and Pseudomonas aeruginosa but only mild effects against the gram-positive bacteria Staphylococcus aureus
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Cu2+
-
enhance interaction with substrate but lower stability
Cu2+
-
crystal structure
K+
-
optimum activity at 30-50 mM
Na+
-
increases activity
Na+
-
NaCl: 0.1-0.25 M optimum concentration
Ni2+
-
-
Ni2+
-
binds the enzyme, crystal structure
Zn2+
-
enhance interaction with substrate but lower stability
K+
-
increases activity
additional information
-
no effect of bivalent cations on enzyme
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(-)-epigallocatechin-3-gallate
-
noncompetitive
1-(2,5-dideoxy-5-(4-carboxypiperidinyl)-beta-D-threo-pentofuranosyl)thymine
-
-
-
1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
-
-
1-(5-deoxy-5-morpholin-4-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
1-(5-deoxy-5-pyrrolidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
1-(5-deoxy-5-[4-(ethoxycarbonyl)piperidin-1-yl]-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
2'(3')Nucleotides
-
-
-
2',3'-dideoxy-3'-(gamma-aminobutyric acid)amino thymidine
-
-
2',3'-dideoxy-3'-D-leucylamino thymidine
-
-
2',3'-dideoxy-3'-glycylamino thymidine
-
-
2',3'-dideoxy-3'-L-alanylamino thymidine
-
-
2',3'-dideoxy-3'-L-histidinylamino thymidine
-
-
2',3'-dideoxy-3'-L-leucylamino thymidine
-
-
2',3'-dideoxy-3'-L-serinylamino thymidine
-
occupies the active site of ribonuclease A and preferential perturbs the pKa value of His-119 by its free amino group as found from 1H NMR studies, compounds with polar amino acid side chains such as Ser-aT, Tyr-aT and Trp-aT (except His-aT) are more efficient inhibitors compared to those having hydrophobic side chains
2',3'-dideoxy-3'-L-tryptophanylamino thymidine
-
compounds with polar amino acid side chains such as Ser-aT, Tyr-aT and Trp-aT (except His-aT) are more efficient inhibitors compared to those having hydrophobic side chains
2',3'-dideoxy-3'-L-tyrosylamino thymidine
-
compounds with polar amino acid side chains such as Ser-aT, Tyr-aT and Trp-aT (except His-aT) are more efficient inhibitors compared to those having hydrophobic side chains
2',3'-dideoxy-3'-L-valinylamino thymidine
-
-
2'-Deoxynucleotides
-
-
-
3'-CMP
-
strong binding by the wild-type enzyme, reduced binding by enzyme mutants T17A and T82A, kinetics, overview
3'-CMP
-
natural product inhibitor, NMR binding analysis, overview
3'-deoxy-3'-[4-(ethoxycarbonyl)piperidin-1-yl] uridine
-
-
3'-deoxy-3'-[4-carboxypiperidin-1-yl] uridine
-
-
3'-TMP
-
a competitive inhibitor analogue of the 3'-CMP and 3'-UMP natural product inhibitors, the enzyme shows very high affinty and strong binding with 3'-TMP. Binding of 3'-TMP is very similar to other natural and nonnatural pyrimidine ligands, so single nucleotide affinity is independent of the presence or absence of a 2'-hydroxyl on the ribose moiety of pyrimidines
3'-UMP
-
natural product inhibitor, NMR binding analysis, overview
3-amino-N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-succinamic acid
-
-
-
3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine
-
binding of two inhibitor molecules in the central cavity of enzyme
4-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-ylcarbamoyl]-butyric acid
-
-
5'-carboxyadenosine
-
-
-
5'-carboxythymidine
-
-
-
5'-deoxy-5'-N-(4-carboxypiperidinyl)thymidine
-
-
-
5'-deoxy-5'-N-(4-carboxypiperidinyl)uridine
-
-
-
5'-deoxy-5'-piperidin-1-ylthymidine
-
-
5'-N-(4-carboxypiperidinyl)-2',3'-didehydro-3',5'-dideoxythymidine
-
-
-
5'-phospho-2'-deoxyuridine-3-diphosphate (P-5)-adenosine-3'-phosphate
-
i.e. pdUppA-3'-p, multi-ns molecular dynamics simulations of enzyme in complex with inhibitor
5-aminoethyluracil
-
-
5-Nitrouracil
-
-
adenosine 5'-phosphate
-
-
arsenite
-
-
ATP
-
5-ATP binds with the adenine occupying the B2 subsite in the manner of an RNA substrate but with the gamma-phosphate at the P1 subsite, crystal structure of the complex with pancreatic ribonuclease A
aurintricarboxylic acid
-
alters the three-dimensional conformation, dissociation constant of ribonuclease A with aurintricarboxylic acid is 2.33 microM
chitosan
-
molecular weight about 6 kDA, complex formation with enzyme due to establishment of 5-6 ion pairs
chloride
-
-
Copolymer of glutamic acid and tyrosine
-
-
-
cytidine-N3-oxide 2'-phosphate
-
-
cytosolic ribonuclease inhibitor
-
with CpA as substrate, both isoenzymes are fully susceptible to inhibition
-
cytosolic ribonuclease inhibitor
-
protects cells against exogenous ribonucleases, variants of pancreatic ribonuclease that evade ribonuclease inhibitor are cytotoxic, molecular evolution of ribonuclease inhibitor suggests to be a means to enhance the cytotoxicity of mammalian ribonucleases
-
cytosolic ribonuclease inhibitor
-
RI, from Sus scrofa, binding of the RI molecule to the N-terminal RNase A entity, analysis of crystal structures of the RIRNase A complex and the SGRSGRSG-RNase A tandem enzyme, PDB-ID 1DFJ, overview
-
Diethylpyrocarbonate
-
among the His residues of RNase A, His48 is not accessible to react with diethylpyrocarbonate
epicatechin
-
0.04 mM, 4.4% inhibition, noncompetitve, CD spectral analysis of complex with enzyme, preferred site of binding is around residues 34-39 with possible hydrogen bonding to K7 and R10
Epicatechin gallate
-
0.04 mM, 12.7% inhibition, noncompetitve, CD spectral analysis of complex with enzyme, preferred site of binding is around residues 34-39 with possible hydrogen bonding to K7 and R10
epigallocatechin
-
0.04 mM, 6.9% inhibition, noncompetitve, CD spectral analysis of complex with enzyme, preferred site of binding is around residues 34-39 with possible hydrogen bonding to K7 and R10
epigallocatechin gallate
-
0.04 mM, 18.4% inhibition, noncompetitve, CD spectral analysis of complex with enzyme, preferred site of binding is around residues 34-39 with possible hydrogen bonding to K7 and R10
folic acid
-
inhibitor when 2',3'-CMP is substrate not when RNA is substrate
green tea catechins
-
noncompetitive
-
HP-RNase antibodies
-
affinity purified polyclonal antibodies against human pancreatic RNase. 94% inhibition with 50 ng
-
Hydrobenzoinphosphate
-
-
inhibit-Ace
-
86% inhibition at 6 U/ml
-
iodoacetate
-
-
iodoacetate
-
-
liver natural inhibitor
-
-
-
Mercury hematoporphyrin
-
-
Mg2+
-
reduces activity in the presence of K+
N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-malonamic acid
-
-
N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-oxalamic acid
-
-
N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-succinamic acid
-
-
NaCl
-
above 0.25 M
NaCl
-
0.15 M or above
NADP+
-
crystal structure of the complex with pancreatic ribonuclease A
NADPH
-
crystal structure of the complex with pancreatic ribonuclease A
oligo(vinylsulfonic acid)
-
potent competitive inhibitor making nearly 8 favorable Coulombic interactions with the enzyme. Oligo(vinylsulfonic acid) is inexpensive and extremely stable. Accoringly oligo(vinylsulfonic acid) has the potential to be useful prophylactic in many chemical, biochemical, and biotechnical experiments involving RNA
oligonucleotides
-
e.g. ApUp
P1,P3-bis(5'-adenosyl) triphosphate
-
crystal structure of the complex with pancreatic ribonuclease A
Penicillin
-
-
Phenylphosphate
-
-
Pholiota nameko polysaccharide
-
linear mixed-type inhibition, noncompetitive inhibition is predominant over competitive inhibition
-
phosphate
-
-
poly(vinylsulfonic acid)
-
-
poly(vinylsulfuric acid)
-
-
Polyanions
-
natural and synthetic, free poly(A), poly(U)
-
putrescine
-
-
-
Pyrophosphate
-
crystal structure of the complex with pancreatic ribonuclease A
ribonuclease inhibitor
-
cytoplasmic
-
ribonuclease inhibitor
-
forms a tight complex with RNase A
-
ribonuclease inhibitor
-
RI, 97% inhibition at 6 U/ml
-
ribonuclease inhibitor
-
-
-
ribonuclease inhibitor
-
extremely tight complex with bovine ribonuclease inhibitor, Kd value 0.69 fM. Kd value of complex with human ribonuclease inhibitor 0.34 fM
-
ribonuclease inhibitor
-
tight complex with human ribonuclease inhibitor, Kd value 0.34 fM. Kd value of complex with bovine ribonuclease inhibitor 35 fM
-
ribonuclease inhibitor
Q27J90, Q27J91
human placental ribonuclease inhibitor; human placental ribonuclease inhibitor
-
ribonuclease inhibitor
-
crystallization data of complex with enzyme, formation of 19 hydrogen bonds results in extreme stability of complex. Kd value 29 * 10-8 nM
-
ribonuclease inhibitor
-
human placental ribonuclease inhibitor, characterization of its tryptophan residues in the complex with the enzyme. The complex formation results in a more heterogenous environment for both of the optically resolved residues W19 and W375. W19 moves slightly toward a more hydrophobic region, ant the environment of W375 becomes less solvent exposed
-
ribonuclease inhibitor
-
-
-
ribonuclease inhibitor CPRI
-
scavenger of pancreatic-type ribonucleases, chemiluminescence assay to determine radical scavenging activities toward different reactive oxygen species (ROS) including superoxide anion, hydroxyl radical, lipid-derived radicals and singlet oxygen
-
ribonuclease protein inhibitor
-
the native enzyme is an equilibrium mixture of two isomers, MxM and M=M. In the former the two subunits swap their N-terminal helices. In the reducing environment of the cytosol, isoform M=M dissociates into monomers, which are strongly inhibited by ribonuclease protein inhibitor, wheras isoform MxM remains as a non-covalent dimer which evades ribonuclease protein inhibitor
-
RNasin
-
50 kDa protein inhibitor isolated from human placenta
-
Selenite
-
-
spermidine
-
RNA-binding enzyme activity is regulated through spermidine-induced changes in the charge and structure of the RNA substrate. Spermidine transiently stabilizes RNA sub-populations by binding both specifically and nonspecifically
spermine
-
at 0.13 mM: inhibition, at 0.02 M: activity towards cyclic substrates and poly(C) is activated, not towards poly(U)
Thiocyanate
P61823
inactivation due to expansion of the enzyme surface and elongation of the catalytic center
trichloroacetic acid
-
partially inactivates
Urea
-
mechanism of inhibition, urea inhibits ribonuclease A competitively over a concentration range from 100 mM to 4.0 M, urea with its high dipolar moment is a competitive inhibitor and a very high concentration (more than 4.0 M) of it could denature the enzyme, beginning the interaction with the protein at the active center
uridine 5'-diphosphate
-
competitive inhibitor
uridine 5'-phosphate
-
competitive inhibitor
vitamin B12
-
-
VO2+
-
in complex with nucleotide monophosphate
additional information
-
not inhibitory: monoglucosamine up to 2 mM
-
additional information
-
not inhibitory: Mg2+, phosphate, EDTA
-
additional information
-
construction of enzyme dimer composed of monomeric units covalently linked by a single amide bond between the side-chains of residues K66 and E9 by incubation of a lyophilized preparation of enzyme under vacuum at 85C. Dimer exhibits a twofold increase in activity over monomeric enzyme and is not inhibited by the cellular ribonuclease inhibitor protein
-
additional information
-
As(III) species, by avid coordination to the cysteine residues of unfolded reduced proteins, can compromise protein folding pathways, monomethylarsenous acid catalyzes the formation of amyloid-like monodisperse fibrils using reduced ribonuclease A
-
additional information
-
agarose gel and precipitation assays show that the spacer length and the pKa of the carboxylic group have an important role in the inhibitory capacity
-
additional information
-
inhibitor synthesis, molecular docking to the enzyme, interaction of inhibitors with hydrogen bonding network formation between His12 and His119 of RNase A, overview
-
additional information
-
inhibitor synthesis, kinetics, and docking, overview
-
additional information
-
enzme-inhibitor binding and interaction analysis, kinetics, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Chloroquine
-
at 0.13 mM
NaCl
-
at 0.1-0.25 M
Sodium citrate
-
-
sulfate
P61823
decreases the distance between the catalytic His residues and increases the globular compactness
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
5.2
7.5
cyclic 2 ',3'-CMP
-
-
0.46
-
cyclic 2',3'-CMP
-
-
1
7
cyclic 2',3'-CMP
-
allosteric model
1
-
cyclic 2',3'-CMP
-
-
5.1
5.9
cyclic 2',3'-CMP
-
-
0.0023
-
cyclic 2',3'-cytidine monophosphate
-
wild-type, pH 5.5, 25C
0.0026
-
cyclic 2',3'-cytidine monophosphate
-
mutant K7H/R10H, pH 5.5, 25C
0.435
-
cyclic 2',3'-cytidine monophosphate
P07998
mutant R4A/K6A/Q9E/D16G/S17N, 25C, pH 5.0
0.44
-
cyclic 2',3'-cytidine monophosphate
P07998
wild-type, 25C, pH 5.0
2.4
3.5
cyclic 2',3'-UMP
-
pancreas
0.31
-
cytidine-2',3'-cyclic monophosphate
-
D121K mutant, pH 5.5, 25C
0.41
-
cytidine-2',3'-cyclic monophosphate
-
F46A mutant, pH 5.5, 25C
0.42
-
cytidine-2',3'-cyclic monophosphate
-
F46L mutant, pH 5.5, 25C
0.45
-
cytidine-2',3'-cyclic monophosphate
-
pH 5.5, 25C, comercial enzyme
0.46
-
cytidine-2',3'-cyclic monophosphate
-
pH 5.5, 25C, type I enzyme
0.46
-
cytidine-2',3'-cyclic monophosphate
-
wild type enzyme, pH 5.5, 25C
0.51
-
cytidine-2',3'-cyclic monophosphate
-
wild type enzyme, pH 5.5, 25C
0.52
-
cytidine-2',3'-cyclic monophosphate
-
D121A mutant, pH 5.5, 25C
0.55
-
cytidine-2',3'-cyclic monophosphate
-
H12E mutant, pH 5.5, 25C
0.58
-
cytidine-2',3'-cyclic monophosphate
-
pH 5.5, 25C, N34A mutant
0.58
-
cytidine-2',3'-cyclic monophosphate
-
Ala(121-124) mutant, pH 5.5, 25C
0.59
-
cytidine-2',3'-cyclic monophosphate
-
D121E mutant, pH 5.5, 25C
0.62
-
cytidine-2',3'-cyclic monophosphate
-
wild type enzyme, pH 5.5, 25C
0.64
-
cytidine-2',3'-cyclic monophosphate
-
F46V mutant, pH 5.5, 25C
0.64
-
cytidine-2',3'-cyclic monophosphate
-
des-(123-124) mutant, pH 5.5, 25C
0.66
-
cytidine-2',3'-cyclic monophosphate
-
des-124 mutant, pH 5.5, 25C
1.7
-
cytidine-2',3'-cyclic monophosphate
-
F120L mutant, pH 5.5, 25C
2
-
cytidine-2',3'-cyclic monophosphate
-
des-(121-124) mutant, pH 5.5, 25C
3.1
-
cytidine-2',3'-cyclic monophosphate
-
des-(122-124) mutant, pH 5.5, 25C
3.9
-
cytidine-2',3'-cyclic monophosphate
-
H12D mutant, pH 5.5, 25C
4
-
cytidine-2',3'-cyclic monophosphate
-
F120W mutant, pH 5.5, 25C
4
-
cytidine-2',3'-cyclic monophosphate
-
H119D mutant, pH 5.5, 25C
7.9
-
cytidine-2',3'-cyclic monophosphate
-
F120A mutant, pH 5.5, 25C
13
-
cytidine-2',3'-cyclic monophosphate
-
F120G mutant, pH 5.5, 25C
0.38
-
cytidinyl-3',5'-adenosine
-
H119D mutant, pH 5.5, 25C
0.5
-
cytidinyl-3',5'-adenosine
-
pH 5.5, 25C, comercial enzyme
0.52
-
cytidinyl-3',5'-adenosine
-
pH 5.5, 25C, type I enzyme
0.67
-
cytidinyl-3',5'-adenosine
-
wild type enzyme, pH 5.5, 25C
0.71
-
cytidinyl-3',5'-adenosine
-
H12D mutant, pH 5.5, 25C
0.74
-
cytidinyl-3',5'-adenosine
-
H12E mutant, pH 5.5, 25C
3.5
-
cytidinyl-3',5'-adenosine
-
F120L mutant, pH 5.5, 25C
7.3
-
cytidinyl-3',5'-adenosine
-
F120W mutant, pH 5.5, 25C
13
-
cytidinyl-3',5'-adenosine
-
F120A mutant, pH 5.5, 25C
0.015
-
pentacytidylic acid
-
mutant K7H/R10H/H12K/H119Q, pH 7.0
0.028
-
pentacytidylic acid
-
mutant K7H/R10H, pH 7.0
0.038
-
pentacytidylic acid
-
wild-type, pH7.0
0.34
-
poly (C)
P07998
wild-type, 25C, pH 5.0
0.47
-
poly (C)
P07998
mutant R4A/K6A/Q9E/D16G/S17N, 25C, pH 5.0
0.0115
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28L
-
0.0135
-
poly(A)-poly(U)
-
pH 7.5, 37C, wild-type enzyme
-
0.0338
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/G38D
-
0.034
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant G38D
-
0.0485
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant R39A
-
0.052
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A
-
0.0566
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28L/R39A
-
0.0572
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/R39A
-
0.0853
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/G38D/R39A
-
0.1059
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant R39A/G38D
-
0.032
-
poly(A)poly(U)
-
mutant K74A, pH 7.5, 37C
-
0.052
-
poly(A)poly(U)
-
mutant K62A, pH 7.5, 37C
-
0.063
-
poly(A)poly(U)
-
wild-type, pH 7.5, 37C
-
0.09
-
poly(A)poly(U)
-
mutant K6A, pH 7.5, 37C
-
0.1
-
poly(A)poly(U)
-
wild type enzyme
-
0.16
-
poly(A)poly(U)
-
mutant R32A, pH 7.5, 37C
-
0.209
-
poly(A)poly(U)
-
G38D mutant
-
0.244
-
poly(A)poly(U)
-
ADA mutant
-
0.314
-
poly(A)poly(U)
-
R4A mutant
-
0.389
-
poly(A)poly(U)
-
K102A mutant
-
0.0409
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/G38D/R39A
0.0435
-
poly(C)
-
pH 7.5, 37C, mutant Q28L/R39A
0.048
-
poly(C)
-
pH 7.5, 37C, mutant G38D
0.0567
-
poly(C)
-
pH 7.5, 37C, mutant R39A
0.0609
-
poly(C)
-
pH 7.5, 37C, mutant R39A/G38D
0.0739
-
poly(C)
-
pH 7.5, 37C, mutant Q28A
0.0804
-
poly(C)
-
pH 7.5, 37C, mutant Q28L
0.0823
-
poly(C)
-
pH 7.5, 37C, wild-type enzyme
0.091
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/G38D
0.0993
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/R39A
0.1
-
poly(C)
-
wild-type, pH 7.5, 37C
0.21
-
poly(C)
-
mutant R32A, pH 7.5, 37C
0.3
-
poly(C)
-
mutant K74A, pH 7.5, 37C
0.37
-
poly(C)
-
mutant K62A, pH 7.5, 37C
0.4
-
poly(C)
-
mutant K6A, pH 7.5, 37C
0.46
0.71
poly(C)
-
wild type and mutant enzyme
1.7
-
poly(C)
-
pH 7.5, 37C, wild-type enzyme
4
-
poly(C)
-
pH 7.5, 37C, mutant enzyme D121A
0.0005
-
tRNA
Q27J90, Q27J91
pH 7.0
0.0172
-
tRNA
Q27J90, Q27J91
pH 7.0
4
-
tRNA
-
pH 7.5, 37C, wild-type enzyme
5
-
tRNA
-
pH 7.5, 37C, mutant enzyme D121A
0.79
-
UpA
-
-
additional information
-
CpA
-
type I and II isoenzymes, almost identical values to those of commercial enzyme, pH 5.5, 25C
3
-
cyclic 2',3'-UMP
-
-
additional information
-
cytidine-2',3'-cyclic monophosphate
-
type I and II isoenzymes, almost identical values to those of commercial enzyme, pH 5.5, 25C
22
-
cytidinyl-3',5'-adenosine
-
F120G mutant, pH 5.5, 25C
additional information
-
additional information
-
second-order rate constants for disulfide bond formation in the oxidative folding of RNase A with DHSox as an oxidant at 25C, overview
-
additional information
-
additional information
-
Michelis-Menten curves and catalytic efficiencies of HPR and its mutant variants on different substrates
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1.5
2.2
cyclic 2',3'-CMP
-
-
1.6
2.5
cyclic 2',3'-CMP
-
-
0.36
-
cyclic 2',3'-cytidine monophosphate
P07998
wild-type, 25C, pH 5.0
0.45
-
cyclic 2',3'-cytidine monophosphate
P07998
mutant R4A/K6A/Q9E/D16G/S17N, 25C, pH 5.0
3.5
-
cyclic 2',3'-cytidine monophosphate
-
mutant K7H/R10H, pH 5.5, 25C
12
-
cyclic 2',3'-cytidine monophosphate
-
wild-type, pH 5.5, 25C
0.6
1.1
cyclic 2',3'-UMP
-
-
27
-
pentacytidylic acid
-
mutant K7H/R10H/H12K/H119Q, pH 7.0
54
-
pentacytidylic acid
-
mutant K7H/R10H, pH 7.0
323
-
pentacytidylic acid
-
wild-type, pH 7.0
13.3
-
poly (C)
P07998
wild-type, 25C, pH 5.0
16
-
poly (C)
P07998
mutant R4A/K6A/Q9E/D16G/S17N, 25C, pH 5.0
1.57
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant R39A/G38D
-
2.23
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/G38D/R39A
-
4.85
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/G38D
-
5.35
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant R39A
-
5.525
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/R39A
-
7.001
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A
-
8.315
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant G38D
-
8.89
-
poly(A)-poly(U)
-
pH 7.5, 37C, wild-type enzyme
-
12.27
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28L
-
14.71
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28L/R39A
-
0.0002
-
poly(A)poly(U)
-
mutant K74A, pH 7.5, 37C
-
0.0012
-
poly(A)poly(U)
-
mutant K6A, pH 7.5, 37C
-
0.0019
-
poly(A)poly(U)
-
wild-type, pH 7.5, 37C
-
0.0026
-
poly(A)poly(U)
-
mutant K62A, pH 7.5, 37C
-
0.0065
-
poly(A)poly(U)
-
mutant R32A, pH 7.5, 37C
-
0.11
-
poly(C)
-
mutant K74A, pH 7.5, 37C
0.192
-
poly(C)
-
mutant K6A, pH 7.5, 37C
0.242
-
poly(C)
-
wild-type, pH 7.5, 37C
0.57
-
poly(C)
-
mutant R32A, pH 7.5, 37C
0.83
-
poly(C)
-
mutant K62A, pH 7.5, 37C
1033
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/G38D
1100
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/G38D/R39A
1233
-
poly(C)
-
pH 7.5, 37C, mutant Q28L/R39A
1500
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/R39A
1650
-
poly(C)
-
pH 7.5, 37C, mutant R39A/G38D
1667
-
poly(C)
-
pH 7.5, 37C, mutant G38D
1833
-
poly(C)
-
pH 7.5, 37C, mutant Q28L
2167
-
poly(C)
-
pH 7.5, 37C, mutant Q28A
2317
-
poly(C)
-
pH 7.5, 37C, wild-type enzyme
2833
-
poly(C)
-
pH 7.5, 37C, mutant R39A
35.7
-
RNA
-
pH 7.0, 37C
0.056
-
tRNA
Q27J90, Q27J91
pH 7.0
2.6
-
tRNA
Q27J90, Q27J91
pH 7.0
2.7
3.7
cyclic 2',3'-UMP
-
-
additional information
-
additional information
-
-
-
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
12
-
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine
-
mutant enzyme M30C/N44C
253923
1044
-
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine
-
mutant enzyme I107C/A122C
253923
1566
-
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine
-
mutant enzyme H105C/V124C
253923
3132
-
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine
-
mutant enzyme A4C/V118C
253923
3480
-
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine
-
mutant enzyme V43C/R85C
253923
4002
-
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine
-
mutant enzyme R10C/R33C
253923
17400
-
6-carboxyfluorescein-dArUdAdA-6-carboxytetramethylrhodamine
-
wild-type enzyme
253923
21.7
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/G38D/R39A
0
28.3
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant R39A/G38D
0
96.7
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/R39A
0
110
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant R39A
0
135
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A
0
143.3
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28A/G38D
0
245
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant G38D
0
260
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28L/R39A
0
658.3
-
poly(A)-poly(U)
-
pH 7.5, 37C, wild-type enzyme
0
1067
-
poly(A)-poly(U)
-
pH 7.5, 37C, mutant Q28L
0
15170
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/R39A
22838
18170
-
poly(C)
-
pH 7.5, 37C, mutant R39A
22838
20170
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/G38D
22838
20670
-
poly(C)
-
pH 7.5, 37C, mutant Q28L
22838
24830
-
poly(C)
-
pH 7.5, 37C, mutant Q28A
22838
26830
-
poly(C)
-
pH 7.5, 37C, mutant Q28A/G38D/R39A
22838
27170
-
poly(C)
-
pH 7.5, 37C, mutant R39A/G38D
22838
28170
-
poly(C)
-
pH 7.5, 37C, wild-type enzyme
22838
28330
-
poly(C)
-
pH 7.5, 37C, mutant Q28L/R39A
22838
40670
-
poly(C)
-
pH 7.5, 37C, mutant G38D
22838
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.08124
-
(-)-epigallocatechin-3-gallate
-
pH 6.0
0.229
-
1-(2,5-dideoxy-5-(4-carboxypiperidinyl)-beta-D-threo-pentofuranosyl)thymine
-
pH 7.5, 25C
-
0.423
-
1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
-
-
0.179
-
1-(5-deoxy-5-morpholin-4-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
0.172
-
1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
0.203
-
1-(5-deoxy-5-pyrrolidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
0.077
-
1-(5-deoxy-5-[4-(ethoxycarbonyl)piperidin-1-yl]-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
-
-
0.08
-
2',3'-dideoxy-3'-L-serinylamino thymidine
-
-
0.451
-
2',3'-dideoxy-3'-L-tyrosylamino thymidine
-
-
0.103
-
3'-deoxy-3'-[4-(ethoxycarbonyl)piperidin-1-yl] uridine
-
-
0.12
-
3'-deoxy-3'-[4-carboxypiperidin-1-yl] uridine
-
-
0.037
-
3-amino-N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-succinamic acid
-
pH 7.5, 25C
-
3.7e-06
-
5'-AMP
-
wild-type, pH 6.0
0.067
-
5'-carboxyadenosine
-
pH 7.5, 25C
-
0.193
-
5'-carboxythymidine
-
pH 7.5, 25C
-
0.162
-
5'-deoxy-5'-N-(4-carboxypiperidinyl)thymidine
-
pH 7.5, 25C
-
0.075
-
5'-deoxy-5'-N-(4-carboxypiperidinyl)uridine
-
pH 7.5, 25C
-
0.396
-
5'-deoxy-5'-piperidin-1-ylthymidine
-
-
6.7e-05
-
5'-GMP
-
wild-type, pH 6.0
0.25
-
5'-N-(4-carboxypiperidinyl)-2',3'-didehydro-3',5'-dideoxythymidine
-
pH 7.5, 25C
-
0.00021
-
chitosan
-
substrate poly(I)poly(C), pH 7.0, 25C
0.00022
-
chitosan
-
substrate poly(C), pH 7.0, 25C
0.1063
-
green tea catechins
-
pH 6.0
-
0.38
-
N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-malonamic acid
-
-
0.132
-
N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-oxalamic acid
-
-
0.918
-
N-[2-hydroxymethyl-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl]-succinamic acid
-
-
1.1e-08
-
oligo(vinylsulfonic acid)
-
without NaCl
0.0004
-
oligo(vinylsulfonic acid)
-
pH 6.0, 0.1 M NaCl
0.2999
-
Pholiota nameko polysaccharide
-
Ki value, pH 7.0, 37C
-
0.545
-
Pholiota nameko polysaccharide
-
alphaKi value, pH 7.0, 37C
-
5.5
-
phosphate
-
F120G mutant, pH 5.5, 25C
6.4
-
phosphate
-
wild type enzyme, pH 5.5, 25C
10
-
phosphate
-
F120A mutant, pH 5.5, 25C; F120L mutant, pH 5.5, 25C
11
-
phosphate
-
F120W mutant, pH 5.5, 25C
0.00024
-
ribonuclease inhibitor
-
G88R mutant, pH 6.0, 25C
-
0.00035
-
ribonuclease inhibitor
-
C40A/G88R/C95A mutant, pH 6.0, 25C
-
0.00042
-
ribonuclease inhibitor
-
PE3 variant, pH 5.5, 25C
-
0.00065
-
ribonuclease inhibitor
-
A4C/G88R/V118C mutant, pH 6.0, 25C
-
0.00077
-
ribonuclease inhibitor
-
PE3I2 variant, pH 5.5, 25C
-
0.00078
-
ribonuclease inhibitor
-
C65A/C72A/G88R mutant, pH 6.0, 25C
-
0.0008
-
ribonuclease inhibitor
-
PE3I1 variant, pH 5.5, 25C
-
0.00134
-
ribonuclease inhibitor
-
PI5 variant, pH 5.5, 25C
-
0.0039
-
ribonuclease inhibitor
-
A4C/C65A/C72A/G88R/V118C mutant, pH 6.0, 25C
-
0.65
-
uridine 5'-diphosphate
-
binds to the active site of the enzyme by anchoring two molecules connected to each other by hydrogen bonds and van der Waals interactions
4
-
uridine 5'-phosphate
-
binds to the active site of the enzyme by anchoring two molecules connected to each other by hydrogen bonds and van der Waals interactions
IC50 VALUE [mM]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.028
-
H2O2
-
oxidative stability of complex with human ribonuclease inhibitor
0.029
-
H2O2
-
oxidative stability of complex with bovine ribonuclease inhibitor
0.042
-
H2O2
-
oxidative stability of complex with human ribonuclease inhibitor
0.3
-
H2O2
-
oxidative stability of complex with bovine ribonuclease inhibitor
additional information
-
additional information
-
radical scavenging activities of CPRI indicated, measured by chemiluminescence, values shown, radical scavenging activities higher than those of tea polyphenols
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.017
-
-
pH 5.0, 37C
1.14
-
-
substrate poly(A)poly(U), dimethyl suberimidate-treated, monomeric RNase A, pH 7.0, 25C
1.55
-
-
substrate poly(A)poly(U), native, monomeric RNase A, pH 7.0, 25C
2.22
-
-
substrate poly(A)poly(U), cross-linked RNase A dimer, pH 7.0, 25C
3
-
-
enzyme monomer after lyophilization
3.52
-
-
pH 7.0, 65C
6.08
-
-
enzyme dimer form I
11.67
-
-
enzyme dimer form I
12.15
-
-
substrate poly(A)poly(U), domain-swapped RNase A C-dimer pH 7.0, 25C
12.67
-
-
substrate yeast RNA, cross-linked RNase A dimer, pH 7.0, 25C
13.33
-
-
substrate yeast RNA, cross-linked RNase A dimer, treated with dimethyl suberimidate, pH 7.0, 25C
25.21
-
-
substrate poly(A)poly(U), cross-linked RNase A dimer, treated with dimethyl suberimidate, pH 7.0, 25C
49.33
-
-
substrate yeast RNA, dimethyl suberimidate-treated, monomeric RNase A, pH 7.0, 25C
53.46
-
-
substrate yeast RNA, domain-swapped RNase A C-dimer pH 7.0, 25C
84.55
-
-
substrate yeast RNA, native, monomeric RNase A, pH 7.0, 25C
1100
-
-
brain, poly(C)
2400
-
-
brain, RNA
10300
-
-
RNA
11300
-
-
pancreas, RNA
22600
-
-
pancreas, poly(C)
35000
-
-
poly(C)
additional information
-
-
type I isoform, 100% specific activity relative to commercial RNase A. Type II isoform, 53% specific activity relative to commercial enzyme
additional information
-
-
isoenzyme D-I shows values of 88 U/mg, 382 U/mg and 6.2 U/mg with yeast RNA, poly(U) and poly(A)poly(U) as substrates, respectively. D-II isoenzyme shows values of 85 U/mg, 387 U/mg and 2.5 U/mg with yeast RNA, poly(U) and poly(A)poly(U) as substrates, respectively
additional information
-
-
for assay conditions ribonuclease A solution prepared by dissolving 8 mg ribonuclease A in 4 ml 0.1 M NaHCO3 at pH 9.5 following by pre-cooling to 3C
additional information
-
-
enzymatic activities of the various RNase A monomeric and zero-length or domain-swapped oligomeric species on single-stranded yeast or double-stranded poly(A)-poly(U) RNA, overview. The dimers show higher activity compared to the monomners
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5
-
-
assay at
5.5
-
-
-
6.5
-
-
25C
7
7.5
-
-
7
-
Q27J90, Q27J91
;
7.3
7.6
-
liver
7.5
-
-
assay at
7.5
-
-
assay at
7.7
-
-
-
7.8
-
-
seminal plasma
8.2
-
-
-
9.5
-
-
assay at
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
3
9
-
pH 3.0: about 10% of activity maximum, pH 9.0: about 5% of activity maximum
6
10
-
pH 6: about 15% of activity maximum, pH 10: about 10% of activity maximum
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
25
-
-
assay at
37
-
-
assay at
60
-
-
-
60
-
-
soluble and immobilized enzyme
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
15
70
-
25C: about 5% of activity maximum, 70C: about 45% of activity maximum
66.6
-
-
melting temperature of complex with human ribonuclease inhibitor
68
-
-
melting temperature of complex with bovine ribonuclease inhibitor
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4.55
-
Q5QJV3
isoelectric focusing
5.1
-
Q5QJV3
calculated
10.1
-
-
calculated
10.2
-
Q27J90, Q27J91
isoform RNase A-1
11
-
Q27J90, Q27J91
isoform RNase A-2; isoform RNase A-2, calculated
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
Q27J90, Q27J91
;
Manually annotated by BRENDA team
-
endothelial cells are the main source of serum enzyme
Manually annotated by BRENDA team
Q5QJV3
specific expression of isoform RNase9, especially in caput and corpus. Expression is andorgen-dependent
Manually annotated by BRENDA team
A5HAK0, A5HAK2, -
weak expression
Manually annotated by BRENDA team
Q27J90, Q27J91
peripheral blood granulocyte; peripheral blood granulocyte
Manually annotated by BRENDA team
A5HAK0, A5HAK2, -
strong expression; strong expression
Manually annotated by BRENDA team
A5HAK0, A5HAK2, -
weak expression; weak expression; weak expression
Manually annotated by BRENDA team
A5HAK0, A5HAK2, -
strong expression; strong expression
Manually annotated by BRENDA team
Capreolus capreolus, Cervus capreolus
-
-
Manually annotated by BRENDA team
-
pancreas cancer cell
Manually annotated by BRENDA team
-
main source of serum enzyme are endothelial cells
Manually annotated by BRENDA team
Q5QJV3
enzyme is bound on the acrosomal domain of sperm
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
the enzyme is secreted
-
Manually annotated by BRENDA team
additional information
-
analysis of synthesis and maturation, folding, quality control, and secretion, of pancreatic RNase in the endoplasmic reticulum of live cells, overview. In contrast to the slow in vitro refolding, the protein folds almost instantly after translation and translocation into the endoplasmatic reticulum lumen. Despite high stability of the native protein, only about half of the RNase reaches a secretion competent, monomeric form and is rapidly transported from the rough endoplasmic reticulum via the Golgi complex to the extracellular space, the rest remains in the endoplasmic reticulum mainly in the form of dimers and is slowly degraded
-
Manually annotated by BRENDA team
additional information
-
analysis of synthesis and maturation, folding, quality control, and secretion, of pancreatic RNase in the endoplasmic reticulum of live cells, overview. Human RNase folds rapidly and is secreted mainly in glycosylated forms
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
11990
-
-
mutant T25R/N26W/L27R analyzed by MALDI-TOF mass spectrometry
13590
-
-
mutant enzyme Y73A, MALDI-TOF/TOF mass spectrometry; mutant enzyme Y97A, MALDI-TOF/TOF mass spectrometry
13600
-
-
mutant enzyme Y25A, MALDI-TOF/TOF mass spectrometry
13610
-
-
mutant enzyme F120A, MALDI-TOF/TOF mass spectrometry; mutant enzyme F46A, MALDI-TOF/TOF mass spectrometry; mutant enzyme F8A, MALDI-TOF/TOF mass spectrometry
13620
-
-
mutant enzyme K7A, MALDI-TOF/TOF mass spectrometry; mutant enzyme M13A, MALDI-TOF/TOF mass spectrometry; mutant enzyme M30A, MALDI-TOF/TOF mass spectrometry; mutant enzyme Q28A, MALDI-TOF/TOF mass spectrometry; mutant enzyme T87A, MALDI-TOF/TOF mass spectrometry
13630
-
-
mutant enzyme Y97L, MALDI-TOF/TOF mass spectrometry
13640
-
-
N34A mutant, mass spectrometry
13640
-
-
mutant enzyme D53A, MALDI-TOF/TOF mass spectrometry; mutant enzyme L35A, MALDI-TOF/TOF mass spectrometry; mutant enzyme L51A, MALDI-TOF/TOF mass spectrometry
13650
-
-
mutant enzyme F46L, MALDI-TOF/TOF mass spectrometry; mutant enzyme F8L, MALDI-TOF/TOF mass spectrometry; mutant enzyme M79A, MALDI-TOF/TOF mass spectrometry
13660
-
-
mutant enzyme V43A, MALDI-TOF/TOF mass spectrometry
13670
-
-
mutant enzyme Y25F, MALDI-TOF/TOF mass spectrometry
13680
-
-
pancreas, amino acid composition
13680
-
-
type I isoenzyme, mass spectrometry
13680
-
-
amino acid sequence
13790
-
-
pancreas, amino acid composition, in vitro synthesized enzyme, precursor protein has a 7000fold higher molecular weight
13850
15310
-
type II isoenzyme, multiple mass peaks, mass spectrometry
14000
24000
-
fractions with one glycosylation site occupied, Asn34, SDS-PAGE
14020
-
-
milk, sedimentation ultracentrifugation
14750
-
-
mutant R4A/K6A/Q9E/D16G/S17N/T36Y/Q37R/G38W analyzed by MALDI-TOF mass spectrometry
15000
-
-
-
15000
-
-
pancreas, gel filtration, SDS-PAGE
15000
-
-
pancreas, ultracentrifugation
15000
-
-
high homology to human angiogenin
18000
26000
-
gel filtration
24000
36000
-
fractions with two or three glycosylation sites occupied, SDS-PAGE
25000
-
-
SDS-PAGE
27200
-
-
seminal plasma, amino acid composition
38300
-
Q5QJV3
PAGE, recombinant protein
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 8582, calculated
?
Q27J90, Q27J91
x * 15767, calculated; x * 15767, calculated
dimer
-
2 * 14000, seminal plasma, SDS-PAGE under reducing conditions
dimer
-
-
dimer
-
gel filtration
dimer
-
two distinct dimeric forms. In one dimer (AA-CS), the two monmomers swap the C-terminal beta-strand (residues 116-124), while in the other (AA-NS) the two monomers mutually exchange the N-terminal alpha-helix
dimer
-
BS-RNase is covalent dimer with two intersubunit disulfide bridges between Cys31 of one chain and Cys32 of the second and vice versa. The native enzyme is an equilibrium mixture of two isomers, MxM and M=M. In the former the two subunits swap their N-terminal helices. In the reducing environment of cytosol, M=M dissociates into monomers, which are strongly inhibited by ribonuclease protein inhibitor, wheras MxM remains as a non-covalent dimer which evades ribonuclease protein inhibitor
dimer
Q5QJV3
2 * 21300, calculated, 2 * 19700, SDS-PAGE of recombinant protein, 2 * 26700, SDS-PAGE of native protein
dimer
-
engineered proteins
dimer
-
analyzed by NMR (DOSY), pH 4.3, low salt conditions (0.1 M KH2PO4), 1.2 mM protein concentraion
dimer
-
engineered protein
dimer
P00669
swapping keeps the dimeric structure stable even in the reducing cytosolic environment
dimer
-
besides dimers, also trimers and higher oligomers can be identified among the products of the covalently linking reaction, and the zero-length dimers appear not to be a unique species, but heterogeneous, overview. Quantification of the zero-length oligomers
monomer
-
1 * 15000, pancreas, SDS-PAGE
monomer
-
1 * 13683, pancreas
monomer
-
analyzed by NMR (DOSY, NOE), neutral pH, 0.3 M NaCl, low micromolar protein concentration (0.18 mM)
oligomer
-
ribonuclease A can form a series of 3D domain swapped oligomers by exchanging the N-terminal alpha-helix or the C-terminal beta-strand or both. These oligomers have additional biological and enzymatic activities that the monomeric protein lacks. Ribonuclease A oligomerization is induced by 40% acetic acid, which has been assumed to mildly unfold the protein by detaching the terminal segments and consequently facilitating intersubunit swapping, once the acetic acid is removed by lyophilization and the protein is redissolved in a benign buffer
monomer
-
primarily
additional information
-
protein disulfide isomerase acts both as chaperone and an oxidase during the folding of enzyme. Protein disulfide isomerase catalyzes the conversion of the kinetically trapped enzyme intermediates, des-[26-84] and des-[58-110], by re-shuffling them into the on-pathway intermediate, des-[40-95], and the formation of the native protein
additional information
-
enzyme aggregates to form various types of catalytically active oligomers during lyophilization from aqueous acetic acid solution. Each oligomeric species is present in at least two conformational isomers. The review briefly describes the structures of the main oligomers of RNase A, and their principal functional and biological properties
additional information
-
by lyophilization from 40% acetic acid solutions, bovine pancreatic ribonuclease A forms three-dimensional domain-swapped dimers, trimers, and tetramers. Each oligomeric species consists of at least two conformers, one less basic, one more basic. Identification of a fifth tetramer, pentamers and hexamers, and detection of trace heptameric, octameric and nonameric species
additional information
-
aggregation of RNaseA might be initiated by hydrophobic interactions, controlled by oligomerization and mediated by electrostatic interactions
additional information
P61991
strong van der Waals interaction energy between residues F5, F31, and Y33
additional information
-
lyophilization of enzyme from 40% acetic acid solution leads to formation of several three-dimensional domain-swapped oligomers, dimers, trimers, tetramers, pentamers. Hexamers, and traces of high-order oligomers. Modeling of tetrameric structure and of larger multimers
additional information
P07998
enzyme variant PM8, in which the sequence of the N-terminal domain has been substituted by that of bovine seminal ribonuclease and Pro101 has been substituted by Glu. At 29C in 20% (v/v) ethanol, a significant portion of PM8 is in dimeric form without formation of higher oligomers. Dissociation constant of this dimer is 5 mM at 29C. A decrease in temperature shifts the monomer-dimer equilibrium to dimer. Model for dimerization with an open interface formed first and then intersubunit interactions stabilize the hinge loop in a conformation that completely displaces the equilibrium between nonswapped and swapped dimers to swapped ones
additional information
-
comparison of folding kinetics with Rana pipiens' onconase and bovine angiogenin at pH 8.0 and 15C. Direct correlation between the number of cis-prolyl bonds in a native protein and the complexity with which it folds via slower phases
additional information
-
comparison of folding kinetics with bovine RNase A and angiogenin at pH 8.0 and 15C. Direct correlation between the number of cis-prolyl bonds in a native protein and the complexity with which it folds via slower phases
additional information
-
lyophilization of enzyme from 50% acetic acid solution leads to formation of two dimers and several oligomeric forms. Study on relationship between surface histidine topography in oligomeric forms and catalytic property. Comparison with seminal ribonucleases. Oligomerization also results in modification of the affinity toward the immobilized transition-metal chelate iminodiacetic acid-Cu(II)
additional information
-
the chemical conjugation of polyethylene glycol to the RNase A C-dimer, and to two trimers, decreases the aspermatogenic activity of the oligomers while increasing their inhibitory activity on the growth of human UB900518 amelanotic melanoma transplanted in athymic nude mice. The conjugated RNase A oligomers are devoid of any embryotoxic activity
additional information
-
construction of enzyme dimer composed of monomeric units covalently linked by a single amide bond between the side-chains of residues K66 and E9 by incubation of a lyophilized preparation of enzyme under vacuum at 85C. Dimer exhibits a twofold increase in activity over monomeric enzyme and is not inhibited by the cellular ribonuclease inhibitor protein
additional information
-
oligomers have similar thermal stability to that of monomeric enzyme, suggesting that the main limiting factor in RNase A stability is the tertiary, rather than quaternary structure
additional information
-
ribonuclease A is capable of forming amyloid-like fibrils, the protein is used as a model system to validate fibrillogenic predictions by a 3D profile method based on the crystal structure of the segment NNQQNYand it is demonstrated that a specific residue order is required for fiber formation
additional information
-
the secreted RNase in the bovine pancreas is mainly monomeric, whereas the enzyme present in the cells also contains 20% dimers
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
glycoprotein
-
serum ribonucleases differ in glycosylation, extent varies from day to day in an individual
glycoprotein
-
type II isoenzyme, O-linked glycoform
glycoprotein
-
unfolding molecular dynamics simulations of glycosylated and unglycosylated enzyme. Attachment of monomeric N-acetylglucosyamine to residue N34 results in a change of denaturing process. The glycosylated enzyme remains more stable due to preserved non-local interactions
glycoprotein
-
3 components, 2 of them are glycosylated
glycoprotein
-
different degrees of glycosylation. The N-glycosylation generates the molecular heterogeneity
glycoprotein
-
pancreatic enzyme has three glycosylation sites, Asn34, Asn76 and Asn88. The majority of the glycans from the normal pancreas enzyme are fucosylated complex biantennary structures. Triantennary and tetrantennary fucosylated glycans are present in the highly glycosylated enzyme fractions, together with traces of glycans with poly-N-acetyllactosamine chains and others. The main core structures of the Capan-1 enzyme are hybrid glycans with branched 3-antenna and biantennary structures containing mainly Gal-GlcNAc chains, both types of compounds substituted with up to three fucose residues and some additionally sialylated. MDAPanc-3 enzyme has sialic acids and fucose linked alpha1-3 and 1-4 to the antennae and core fucose, and galactose residues linked beta1-4 to GlcNAc
glycoprotein
-
RNase 1 from human healthy pancreas contains only neutral glycans, whereas RNase 1 from pancreas cancer cell lines contains sialylated structures. In serum from patients with pancreatic cancer, there is an increase of 40% in core fucosylation in the main sialylated biantennary glycans of RNase 1
glycoprotein
-
presence of N-glycans, three sequons for N-linked glycosylation
glycoprotein
-
3 distinct forms: A, B, C, B and C: glycoproteins, A: not; B-from contains 2 N-acetylglucosamine and 6 mannose residues, C-form contains in addition galactose, and fucose
glycoprotein
-
-
glycoprotein
-
-
glycoprotein
-
presence of N-glycans, one sequon for N-linked glycosylation
additional information
-
native enzyme contains four intra-molecular disulfide bonds. Protein disulfide isomerase catalyzes the conversion of the kinetically trapped enzyme intermediates, des-[26-84] and des-[58-110], by re-shuffling them into the on-pathway intermediate, des-[40-95], and the formation of the native protein
glycoprotein
Q5QJV3
sequence contains a potential N-glycosylation site at N177
additional information
-
protein exhibits some degree of monomethylation at residues K4 and K6
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
3D domain-swapped dimer
-
ammonium sulfate precipitation, crystal structure of the cis-Pro to Gly variant P114G, structure solved at 2.0 A resolution, space group: P4(3)2(1)2
-
at 1.33 A resolution, space group P31. Structure contains two molecules of nucleotide per enzyme molecule, one in the active site cleft in the productive binding mode, the other occupies the pyrimidine-specific binding site in a non-productive mode
-
bovine pancreatic ribonuclease A is crystallized from a mixture of small molecules containing basic fuchsin, tobramycin and uridine 5-monophosphate. Solution of the crystal structure reveals that the enzyme is selectively bound to uridine 5-monophosphate, with the pyrimidine ring of uridine 5-monophosphate residing in the pyrimidine-binding site at Thr45, description of the mode of binding of the nucleotide to the enzyme, crystal structure of bovine pancreatic ribonuclease complexed with uridine-5-monophosphate at 1.60 A resolution, 0.1 M HEPES buffer, reservoir of 25% PEG3350 in water, droplets are 5-10 mM in basic fuchsin, tobramycin, uridine-5-monophosphate and 1 mM in ribonuclease A, pH 7.0, vapor diffusion, sitting drop, temperature 298 K
-
circular dichroism study on the conformation of enzyme in a miniemulsion. The addition of poly(vinyl alcohol) as a co-surfactant is effective in preserving the protein structural integrity
-
comparison of mutant crystal structures, PDB IDs 3RSK, 1A5P, and 1C9V, with the wild-type structure, PBD ID 1FS3, overview
-
crystallization in presence of 2'-deoxycitidylyl(3'-5')-2'-deoxyadenosine at 4C by using sitting drop vapor diffusion method. Crystal structure of the MxM isomer of the enzyme in the non-covalent dimer form, carboxyamidomethylated at residues Cys31 and Cys32, in a complex with 2'-deoxycitidylyl(3'-5')-2'-deoxyadenosine
-
data of enzyme dimer composed of monomeric units covalently linked by a single amide bond between the side-chains of residues K66 and E9 by incubation of a lyophilized preparation of enzyme under vacuum at 85C. Procedure does not induce a significant conformational change
-
explicit-solvent molecular dynamics simulations up to the melting temperature of 64C. Between 37C and 47C, there is a small but significant decrease in the number of native contacts, beta-sheet hydrogen bonding, and deviation of backbone conformation, and an increase in the number of non-native contacts. At 57CC and 67C, a non-native helical segment of residues 15-20 forms
-
hanging drop vapor diffusion method
-
hanging drop vapor diffusion method, ammonium sulfate, sodium chloride, sodium acetate, pH 6.0, crystal structure of bovine pancreatic ribonuclease A (wild-type), resolution 1.60 A, crystal structure of bovine pancreatic ribonuclease A variant V47A, resolution 1.60 A, crystal structure of bovine pancreatic ribonuclease A variant V54A, resolution 1.60 A, crystal structure of bovine pancreatic ribonuclease A variant V57A, resolution 1.60 A, crystal structure of bovine pancreatic ribonuclease A variant I81A, resolution 2.0 A, crystal structure of bovine pancreatic ribonuclease A variant I106A, resolution 1.40 A, crystal structure of bovine pancreatic ribonuclease A variant V108A, resolution 1.60 A, space group P3221
-
hanging-drop vapor-diffusion method
-
hanging-drop/vapor-diffusion method, 20% PEG 4000, 0,02 M sodium citrat buffer, pH 5.5, 16C, pancreatic ribonuclease A-5-ATP complex, resolution 1.70 A, pancreatic ribonuclease A-P3-bis(5-adenosyl) triphosphate complex, resolution 2.40 A, pancreatic ribonuclease A-NADPH complex, resolution 1.70 A, pancreatic ribonuclease A-NADP complex, resolution 1.70 A, pancreatic ribonuclease A-pyrophosphte ion complex, resolution 1.80 A, space group C121
-
in complex with Cu2+ and Ni2+
-
in complex with inhibitor 3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine at 1.7 A resolution. Two inhibitor molecules bind in the central cavity of enzyme, the first occupying the purine-preferring site, and the second molecule binding to the carboxyl group at the pyrimidine recognition site
-
in complex with inhibitor cytidine-N(3)-oxide 2'-phosphate
-
multi-ns molecular dynamics simulations of enzyme in complex with inhibitor 5'-phospho-2'-deoxyuridine-3-pyrophosphate (P-5)-adenosine-3-phosphate. The adenylate 5'-beta-phosphate binding position and the adenosine syn orientation constitute robust structural features in the complex
-
multiple solvent crystal structures, vapor diffusion, hanging drop, PEG 4000, sodium citrate, pH 5.0, temperature 291 K, crystal structure of crosslinked ribonuclease A, resolution 1.65 A, crosslinked crystals are then transferred with a cryo-loop to new drops containing stabilization buffer and an organic solvent and allowed to soak for 1-2 h at room temperature. Soaked crystals are then collected, cryo-protected by dunking in stabilization buffer containing 20% glycerol, and flash frozen in liquid nitrogen, crystal structure of ribonuclease A in 50% dimethylformamide, resolution 1.84 A, crystal structure of ribonuclease A in 50% dioxane, resolution 1.95 A, crystal structure of ribonuclease A in 70% dimethyl dulfoxide, resolution 1.76 A, crystal structure of ribonuclease A in 70% 1,6-hexanediol, resolution 2.00 A, crystal structure of ribonuclease A in 70% isopropanol, resolution 2.02 A, crystal structure of ribonuclease A in 70% t-butanol, resolution 1.68 A, crystal structure of ribonuclease A in 50% trifluoroethanol, resolution 1.93 A, crystal structure of ribonuclease A in 1 M trimethylamine N-oxide, resolution 1.68 A, crystal structure of ribonuclease A in 50% R,S,R-bisfuranol, resolution 1.76 A, comparison of the multiple solvent crystal structures with inhibitor-bound crystal structures of ribonuclease A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site, investigation of plasticity, hydration and clustering of organic solvent molecules in the active site
-
mutant V43C/R85C at 1.6 A resolution. Residues V43 and R85 are not involved in the folding/unfolding transition states ensemble, and residues A4 and V118 may form non-native contacts
-
neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A, 50% tert-butyl alcohol, temperature 298 K, then the crystal is soaked in heavy water solution, pH 6.2, for two months, BATCH, space group P1211, resolution 1.7 A, His12 acts mainly as a general base in the catalytic process of Rnase A, numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines are also determined
-
of mutants
-
pressure tuning hole burning experiments using the UV-absorbing tyrosine residues. Ribonuclease A protein stays intact upon cooling to 2 K. Its various tyrosine sites show characteristic features which can be resolved in pressure tuning hole burning spectra. Reducing the sulfur bridges leads to a loss of the individual features, and the sites become alike. The respective compressibility is reduced by more than a factor of 2 and comes close to the value of free tyrosine in solution. Compared to the reduction of the sulfur bridges, the influence of guanidinium hydrochloride on the pressure tuning behavior is less pronounced
-
purification
-
ribonuclease A in complex with thymidine 3'-monophosphate, hanging drop vapor diffusion method, 0.002 ml of 80 mg/ml protein in 20% ethanol and 20% acetic acid at pH 5.5, is mixed with 0.004 ml of 3'-TMP dissolved in a mother liquor solution of 20% ammonium sulfate and 2 M sodium chloride at pH 5.5, room temperature, 1 week, X-ray diffraction structure determination and analysis at 1.55 A resolution, molecular replacement, modelling
-
RNase A tandem enzymes, hanging drop vapor diffusion method, mixing of 0.002 ml of 10 mg/ml protein in 10 mm Tris-HCl, pH 7.0, with 0.002 ml of reservoir solution containing 30% w/v PEG 8000 and 200 mm (NH4)2SO4, 6 days, 13C, X-ray diffraction structure determination and analysis at 1.68 A resolution
-
vapor diffusion, hanging drop, PEG 4000, sodium citrate, pH 5.5, 289 K, space group C121,ribonuclease A-1-{5-deoxy-5-[4-(ethoxycarbonyl)piperidin-1-yl]-alpha-L-arabinofuranosyl}pyrimidine-2,4(1H,3H)-dione complex, resolution 1.58 A, ribonuclease A-1-(5-deoxy-5-morpholin-4-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione, resolution 1.60 A, ribonuclease A-1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione, resolution 1.60 A, ribonuclease A-1-(5-deoxy-5-pyrrolidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione, resolution 1.60 A, ribonuclease A-5-deoxy-5-piperidin-1-ylthymidine, resolution 1.72 A, ribonuclease A-1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione, resolution 1.98 A
-
vapor-diffusion, hanging-drop, PEG 4000, sodium citrate, pH 5.5, temperature 289 K, ribonuclease A-uridine 5 phosphate complex, resolution 1.39 A, space group C121, ribonuclease A-uridine 5 diphosphate complex, resolution 1.40 A, space group C121
-
in complex with ribonuclease inhibitor protein, at 1.95 A resolution. Formation of 19 hydrogen bonds results in an extremely stable complex. Residues R39 and R91 are especially involved in complex stability
-
vapor-diffusion technique
-
wild-type in complex with oligonucleotide d(AUGA) at 1.9 A resolution, mutant T89N/E91A in complex with 5'-AMP at 1.65 A resolution. In wild-type, residue E91 forms two hydrogen bonds with the guanine nucleobase in d(AUGA), and T89 is in close proximity to that nucleobase. One nucleic acid molecule is bound to one enzyme molecule. In the mutant, four 5'-AMP molecules are bound to each enzyme molecule in a non-productive mode
-
of the recombinant protein
-
determination of solution structure of mutant F31A by NMR spectroscopy reveals the change in orientation of the W23 side chain, which in the wild type is completely exposed to the solvent, whereas in the mutant is largely buried in the aromatic cluster. Mutation leads to strong distortion in the alpha-sheets with loss in several hydrogen bonds, and increased flexibility of some stretches of the backbone
P61991
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
2
-
-
activity remains below pH 2
7
9
-
maximum conformational stability to urea and guanidine hydrochloride denaturation
7
-
-
enzyme is very stable near neutral pH values
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
-20
90
P61991
wild-type enzyme is extremely stable under all conditions of temperature and pressure applied. Thermodynamic analysis of heat and cold denaturation
32.1
-
-
mutant K74A, first melting temperature
35
40
-
outer shell of ribonuclease structure begins to unfold, steps in pathway of thermal unfolding
37
-
-
30 min
40
70
-
oligomers have similar thermal stability to that of monomeric enzyme, suggesting that the main limiting factor in RNase A stability is the tertiary, rather than quaternary structure
43.1
-
-
melting temperature, mutant I106A
43.3
-
-
melting temperature, mutant V108A
45
-
-
melting temperature, mutant V47A
47.7
-
-
melting temperature, mutant I107A; melting temperature, mutant I81A
48.7
-
-
melting temperature, mutant V57A
49.8
-
-
melting temperature, mutant V54A
51
-
-
melting temperature, mutant N67D/N88A/G89D/R91D; melting temperature, mutant R39D/N67D/N88A/R91D
51.8
-
-
mutant K74A, second melting temperature
52.5
-
-
melting temperature, mutant V118A
53.2
-
-
mutant K62A, melting temperature
54
-
-
melting temperature, mutant R39D/N67D/G89D/R91D
54.5
-
-
mutant K6A, melting temperature
54.8
-
-
wild-type, melting temperature
54.8
-
-
melting temperature, mutant V116A
55
-
-
mutant R32A, melting temperature
57
-
-
melting temperature, mutant R39D/N67D/N88A/G89D; melting temperature, mutant R39D/N88A/G89D/R91D; melting temperature, wild-type
58
-
-
melting temperature, wild-type
58
-
-
melting temperature, mutant R39D/N67D/N88A/G89D/R91D
58.1
-
-
melting temperature, mutant V63A
60
-
-
no loss of activity after 50 min, pH 5
61
-
-
melting temperature, mutant G38R/R39G/N67R/N88R
64.2
-
-
melting temperature of complex with human ribonuclease inhibitor
65
-
-
1 min, complete inactivation
65
-
-
melting temperature, mutant R39L/N67L/N88A/G89L/R91L
65
-
-
antibodies against native RNase or against RNase N-terminal dodecapeptide are effective in lowering aggregation at 65C
68.6
-
-
melting temperature of complex with bovine ribonuclease inhibitor
69.4
-
-
mutant C87A/C104A, melting temperature
69.6
-
-
mutant F36A, melting temperature
70
80
-
immobilized enzyme retains a far greater fraction of activity at higher temperature with respect to the soluble enzyme
77.4
-
-
mutant F28T, melting temperature
78.1
-
-
mutant F28A, melting temperature
79.2
-
-
mutant F36Y, melting temperature
80
-
-
stable up to
85
-
-
stable up to
87
-
-
mutant Glp1E, melting temperature
87.7
-
-
mutant Glp1P, melting temperature
88.5
-
-
wild-type, melting temperature
additional information
-
-
all substitutions produce a decrease in the thermal stability of the variants
additional information
-
-
type I isoenzyme, Tm of 59C. Type II isoenzyme, Tm of 53C
additional information
-
-
mutant enzymes are less stable than the wild type enzyme
additional information
-
-
des-124, des-(123-124), des-(122-124) mutants are 3-6C less stable to thermal denaturation with respect to the wild type enzyme. des-(121-124) mutant is 14C less stable to thermal denaturation with respect to the wild type enzyme
additional information
-
-
His12 mutants enzymes show low thermal stability, with a Tm of 45C. Wild type enzyme and His119 mutant show a Tm of 61C
additional information
-
-
the four extra amino acid residues in the C-terminal region of the enzyme are proposed to be responsible for a decrease in thermal stability
additional information
-
-
two distinct dimeric forms. In one dimer (AA-CS), the two monmomers swap the C-terminal beta-strand (residues 116-124), while in the other (AA-NS) the two monomers mutually exchange the N-terminal alpha-helix. Thermal denaturation of both dimers can be described by a two-step dissociation/unfolding mechanism. The structural determinants for the higher stability of AA-NS should reside in its open interface
additional information
-
-
4-chlorobutan-1-ol induces reversible thermal transition in ribonuclease A at low concentrations, irreversible at intermediate concentrations (50-250 mM) and again reversible transitions at further higher concentrations of the alcohol (250-400 mM)
additional information
-
-
the extremely high thermodynamic stability of enzyme is due to a dramatic deceleration of the unfolding reaction
additional information
-
-
explicit-solvent molecular dynamics simulations up to the melting temperature of 64C. Between 37C and 47C, there is a small but significant decrease in the number of native contacts, beta-sheet hydrogen bonding, and deviation of backbone conformation, and an increase in the number of non-native contacts. At 57C and 67C, a non-native helical segment of residues 15-20 forms
additional information
-
-
heat and pressure produce only slightly different energetic changes in the unfolded state of enzyme. Stability differences in mutants can be attributed to both hydrophobic interactions and packing density
additional information
-
-
analysis of conformational changes by picosecond time-resolved fluorescence of the six tyrosine residues. Upon thermal or chemical unfolding only Y25, Y92, and Y76 undergo significant displacement from their nearest -SS- bridge. A single unfolding event around 59C affects all these residues similarly
additional information
-
-
analysis of thermal unfolding shows a step-wise thermal denaturation mechanism in which the structural adjustment of the N-terminal and the opening of the central structure come before the main unfolding process. Non-native turns form along with the unfolding of the native strucutures. The central region is the most stable part
additional information
-
-
Fourier transformation study of thermal denaturation in D2O solution, using sample-sample two-dimensional correlation spectroscopy and principal component analysis. Enzyme undergoes a pretransition at 46C as well as a main transition at 66C
additional information
-
-
The thermal stability of ribonuclease A and its variants is investigated by circular dichroism spectroscopy measurements. Thermal unfolding proves to be reversible and follows a two-state transition model as judged from the fit of the data. While H105C/V124C-ribonuclease A, the variant with the disulfide bond homolog to onconase is as stable as ribonuclease A and A4C/V118C- and V43C/R85C-ribonuclease A are more stable than ribonuclease A, R10C/R33C-, I107C/A122C-, and particularly M30C/N44C-ribonuclease A are destabilized in comparison to ribonuclease A
additional information
-
-
thermal denaturation profiles of the wild-type enzyme and its mutant variants, overview
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, phosphate buffer, no salts stabilize
-
2 M guanidine, activity remains
-
4-chlorobutan-1-ol induces reversible thermal transition in ribonuclease A at low concentrations, irreversible at intermediate concentrations (50-250 mM) and again reversible transitions at further higher concentrations of the alcohol (250-400 mM)
-
5% trichloroacetic acid partially inactivates
-
8 M urea, activity remains
-
calculation of thermodynamic parameters from thermally induced unfolding curves
-
Cu2+, binding of Cu2+ lowers stability to thermal and urea denaturation
-
guanidine hydrochloride causes denaturation
-
LiBr causes denaturation
-
LiCl, denaturation
-
LiClO4, denaturation
-
methanol has no effect of refolding properties
-
oligomers have similar thermal stability to that of monomeric enzyme, suggesting that the main limiting factor in RNase A stability is the tertiary, rather than quaternary structure
-
trichloroacetic acid
-
two distinct dimeric forms. In one dimer (AA-CS), the two monmomers swap the C-terminal beta-strand (residues 116-124), while in the other (AA-NS) the two monomers mutually exchange the N-terminal alpha-helix. The two dimers are metastable and dissociate spontaneously to monomers with different kinetics
-
urea, denaturation, urea interferes with interhydrophobic interactions by affecting the water molecules
-
urea, low concentrations of salts, CaCl2, LiClO4 or LiCl, stabilize against urea denaturation at higher concentration they destabilize
-
Zn2+, binding of Zn2+ lowers stability to thermal and urea denaturation
-
immobilized enzyme retains 40-80% activity when incubated 30 min at 55C with trypsin
-
24 h, 125 mM H2SO4, no loss of activity
-
enzyme is resistant to unfolding by 8 M urea. It can only be unfolded by guanidinium chloride at high concentrations or by a combinantion of acid and thermally induced denaturation
-
wild-type enzyme is extremely stable under all conditions of temperature and pressure applied. Thermodynamic analysis of heat and cold denaturation
P61991
ORGANIC SOLVENT
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
acetic acid
-
lyophilization of enzyme from 40% acetic acid solution leads to formation of several three-dimensional domain-swapped oligomers, dimers, trimers, tetramers, pentamers. Hexamers, and traces of high-order oligomers. Modeling of terameric structure and of larger multimers
Ethanol
P07998
at 29C in 20% (v/v) ethanol, a significant portion of enzyme variant PM8, in which the sequence of the N-terminal domain has been substituted by that of bovine seminal ribonuclease and Pro101 has been substituted by Glu is in dimeric form without appearance of higher oligomers
urea
-
no helical structure is found in 8 M urea at pH 2.5, ribonuclease A can oligomerize after thorough unfolding in concentrated solutions of urea, followed by a gel filtration step, which exchanges the denaturant for a refolding buffer. The yield of ribonuclease A oligomers depends on the logarithm of ribonuclease A concentration during refolding.
urea
-
photo-CIDNP NMR spectroscopy for monitoring of the real-time refolding of ribonuclease A following dilution from a high concentration of urea denaturant
guanidine-HCl
-
real-time photo-CIDNP spectra from guanidine-HCl refolding experiments
additional information
-
thermal transition temperature in various solvents
additional information
-
The conformation of ribonuclease A in 40% acetic acid is found to be mostly but not completely unfolded. All X-Pro bonds are predominantly in the trans conformation and the hydrophobic core and the beta-sheet structure unfold completely. However, three alpha-helices are partly populated in ribonuclease A in 40% acetic acid in approximately the same positions as the three native helices.
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C or -70C, loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
cation exchange chromatography
-
chromatography on Mono S column
-
gel filtration
-
gel filtration and cation exchange chromatography
-
of M13 phage displaying RNase A
-
of the mutant proteins
-
of the mutant recombinant proteins
-
purification of RNase A oligomers by cation exchange chromatography
-
purification of the covalent RNase A oligomers by two-step cation exchange chromatography and two gel filtration steps
-
recombinant wild-type and mutant enzymes from Escherichia coli
-
partial
-
affinity chromatography on heparin column and reversed-phase chromatography
-
gel filtration on a Mono S HR 5/5 FPLC column
-
gel filtration on SP-Sepharose column
-
of the recombinant protein
-
partial
-
gel filtration of crude egg extracts, a two-phase polymer system composed of 12.5% PEG 1000 and 12.5% dibasic potassium phosphate added to crude extracts prior to further purification by small-scale cross-axis coil planet centrifuge
P14626
of the recombinant and mutant protein
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
angiogenin/RNase A hybrid protein, overexpression in Escherichia coli
-
expression in Escherichia coli strain BL21
-
expression in Neurospora crassa, seven different vectors are constructed that vary in the use of promoters, open reading frames, and terminators, ccg1 and cfp promoters provide superior efficiency for recombinant gene expression
-
expression in Nicotiana tabacum as a protection against tobacco mosaic virus
P61823
expression in Pichia pastoris
-
expression of mutant protein in Escherichia coli
-
expression of mutants in Escherichia coli
-
expression of the fusion protein with the minor coat protein of phage M13 in M13
-
expression of wild-type and mutant enzymes in Escherichia coli
-
RNase expression in CHO cells
-
expression in Escherichia coli; expression in Escherichia coli
Q27J90, Q27J91
expression in CHO cells
-
expression in Escherichia coli
-
expression of wild-type and mutant enzymes in Escherichia coli
-
RNase expression in CHO cells
-
onconase/RNase A hybrid protein, expression in Escherichia coli
-
expression in Escherichia coli
-
expression in Escherichia coli and Saccharomyces cerevisiae. Recombinant proteins are indistinguishable from the Sulfolobus solfataricus enzyme on the basis of heat stability, pH optimum and RNA digestion pattern as well as NMR analysis, the only exceptions being that residues K4 and K6 are not methylated in the recombinant enzyme
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
A20P
-
thermodynamic and kinetic stability is similar to wild-type ribonuclease A. Mutation has no significant effect on the native conformation and catalytic activity
A20P/S21P
-
thermodynamic and kinetic stability is similar to wild-type ribonuclease A. Mutation has no significant effect on the native conformation and catalytic activity
A4C/V118C
-
site-directed mutagenesis
C40A/C95A
-
disorder in conformation
C40A/C95A
-
comparison of mutant crystal structure, PDB ID 1A5P, with the wild-type structure, PBD ID 1FS3
C65A/C72A
-
loss of cysteines destabilizes regeneration pathway
C65S/C72S
-
loss of cysteines destabilizes regeneration pathway
D121A
-
with nearly the same Km value as the wild type enzyme but with lower hydrolytic activity
D121A/S123A/V124A
-
mutant in which all of the C-terminal four amino acid residues are replaced by alanine residues, with a final lower hydrolytic activity
D121E
-
with nearly the same Km value as the wild type enzyme but with with lower hydrolytic activity
D121K
-
with nearly the same Km value as the wild type enzyme but with with lower hydrolytic activity
D53A
-
slight stabilization, increases the helix propensity of alpha-helix 3
DELTA121-124
-
C-terminal deletion mutant, 14C less stable to thermal denaturation than the wild type enzyme
DELTA122-124
-
C-terminal deletion mutant, 3-6C less stable to thermal denaturation than the wild type enzyme
DELTA123-124
-
C-terminal deletion mutant, 3-6C less stable to thermal denaturation than the wild type enzyme
DELTA124
-
C-terminal deletion mutant, 3-6C less stable to thermal denaturation than the wild type enzyme
E9A
-
site-directed mutagenesis
F120A
-
with less thermal stability than the wild type enzyme
F120A
-
mutant with decreased activity
F120A
-
destabilization
F120G
-
with less thermal stability than the wild type enzyme
F120G
-
mutant with decreased activity
F120L
-
with less thermal stability than the wild type enzyme
F120W
-
with less thermal stability than the wild type enzyme
F120W
-
mutant with decreased activity
F46A
-
mutant with adversely affected conformational stability and folding speed
F46A
-
equivalent destabilization for F46A and F46L variants
F46L
-
mutant with adversely affected conformational stability and folding speed
F46L
-
equivalent destabilization for F46A and F46L variants
F46V
-
mutant with adversely affected conformational stability and folding speed
F46Y
-
thermodynamic and kinetic stability of the mutant is greatly decreased. Mutation has no significant effect on the native conformation and catalytic activity
F8A
-
substitution of Phe8 results in a recombinant variant significantly destabilized
F8L
-
substitution of Phe8 results in a recombinant variant significantly destabilized
G88R
-
mutant with similar thermal stability to wild type enzyme
H105C/V124C
-
site-directed mutagenesis
H119A
-
active-site mutation
H119A/P114G
-
site-directed mutagenesis
H119A/P93A
-
site-directed mutagenesis
H119D
-
with little effect on thermal stability
H12A
-
comparison of mutant crystal structure, PDB ID 1C9V, with the wild-type structure, PBD ID 1FS3
H12D
-
with lower thermal stability than the wild type enzyme
H12E
-
with lower thermal stability than the wild type enzyme
H12K/H119Q
-
0.007% of wild-type activity
I106A
-
detailed study on thermodynamic parameters
I106A
-
thermodynamic analysis of pressure-unfolding and kinetics for positive pressure-jumps
I106A
-
site-directed mutagenesis
I107A
-
detailed study on thermodynamic parameters
I107A
-
thermodynamic analysis of pressure-unfolding and kinetics for positive pressure-jumps
I107C/A122C
-
site-directed mutagenesis
I81A
-
detailed study on thermodynamic parameters
I81A
-
thermodynamic analysis of pressure-unfolding and kinetics for positive pressure-jumps
I81A
-
site-directed mutagenesis
K31A/R33S
-
thermodynamic and kinetic stability of the mutant is greatly decreased. Mutation has no significant effect on the native conformation and catalytic activity
K31A/R33S/F46Y
-
thermodynamic and kinetic stability of the mutant is greatly decreased. Mutation has no significant effect on the native conformation and catalytic activity
K31C/S32C
P00669
site-directed mutagenesis, very poor cytotoxic activity
K31C/S32C/A20S/A19P/T17N/S16G
-
dimeric variant
K31C/S32C/S16G/T17N/A19P/A20S
P00669
site-directed mutagenesis, very poor cytotoxic activity
K31C/S32C/S16G/T17N/A19P/A20S/S80R
P00669
site-directed mutagenesis, very poor cytotoxic activity
K31C/S32C/S80R
P00669
site-directed mutagenesis, very poor cytotoxic activity
K66A
-
site-directed mutagenesis, no intramolecular bonds form in the K66A variant
K7A
-
slight stabilization, increases the helix propensity of alpha-helix 1
K7A/R10A/K66A
-
comparison of mutant crystal structure, PDB ID 3RSK, with the wild-type structure, PBD ID 1FS3
K7H/R10H
-
17% of wild-type activity, introduction of a putative new catalytic site resulting in increase in exonucleolytic activity
K7H/R10H/H12K/H119Q
-
9% of wild-type activity due to suppression of native active site, increase in exonucleolytic activity
L35A
-
thermodynamic and kinetic stability of the mutant is greatly decreased. Mutation has no significant effect on the native conformation and catalytic activity
L35A
-
less destabilizing than M30A substitution
L35A/F46Y
-
thermodynamic and kinetic stability of the mutant is greatly decreased. Mutation has no significant effect on the native conformation and catalytic activity
L35M
-
unchanged in respect to folding and stability, but with enhanced glycosylation
L35S
-
thermodynamic and kinetic stability of the mutant is greatly decreased. Mutation has no significant effect on the native conformation and catalytic activity
L35S/F46Y
-
thermodynamic and kinetic stability of the mutant is greatly decreased. Mutation has no significant effect on the native conformation and catalytic activity
L51A
-
shortening the side chain of the hydrophobic solvent-exposed residue Leu51 to Ala has almost no effect in the stability of ribonuclease A
M13A
-
critical position for the ribonuclease A stability
M30A
-
critical position for the ribonuclease A stability
M30C/N44C
-
site-directed mutagenesis
N113S
-
the mutant N113S is more prominent in the Golgi than wild-type bovine RNase, which is mainly present in the endoplasmic reticulum
N34A
-
unglycosylated mutant
N34D
-
thermodynamic and kinetic stability is similar to wild-type ribonuclease A. Mutation has no significant effect on the native conformation and catalytic activity
P114A
-
site-directed mutagenesis, the mutant adopts a trans conformation in contrast to the wild-type which shows a cis conformation
P114G
-
three hydrogen bonds and two bifurcated hydrogen bonds present in the cis wild-type structure are replaced by four hydrogen bonds and two bifurcated hydrogen bonds in the P114G structure
P114G
-
site-directed mutagenesis, the mutant adopts a trans conformation in contrast to the wild-type which shows a cis conformation
P114G
-
site-directed mutagenesis, the mutant adopts a trans conformation in contrast to the wild-type who shows a cis conformation. The P114G mutant readily domain swaps under physiological conditions in contrast to the wild-type enzyme. The P114G variant has decreased protection from hydrogen exchange compared to the wild-type protein near the C-terminal hinge region. Structure of RNase A P114G with HX fluctuation, overview
P93A
-
disorder in conformation
P93A
-
site-directed mutagenesis
Q28A
-
promotes an increase in the helix propensity, from 0.99 in the wild-type to 1.5
Q28L/K31C/S32C
-
dimeric variant
Q28L/K31C/S32C/A19P
-
dimeric variant
R10C/R33C
-
site-directed mutagenesis
S21L
-
thermodynamic and kinetic stability is similar to wild-type ribonuclease A. Mutation has no significant effect on the native conformation and catalytic activity
S21P
-
thermodynamic and kinetic stability is similar to wild-type ribonuclease A. Mutation has no significant effect on the native conformation and catalytic activity
T17A
-
site-directed mutagenesis, the mutant shows reduced affinity and binding to inhibitor 3'-CMP compared to the wild-type enzyme, kinetics, and conformational exchange motions, overview
T82A
-
site-directed mutagenesis, the mutant shows reduced affinity and binding to inhibitor 3'-CMP compared to the wild-type enzyme, kinetics, and conformational exchange motions, overview
T87A
-
no effect in the protein stability
V108A
-
detailed study on thermodynamic parameters
V108A
-
thermodynamic analysis of pressure-unfolding and kinetics for positive pressure-jumps
V108A
-
site-directed mutagenesis
V116A
-
detailed study on thermodynamic parameters
V118A
-
detailed study on thermodynamic parameters
V124A
-
C-terminus involved in the formation of disulfide bonds during refolding process
V124E
-
C-terminus involved in the formation of disulfide bonds during refolding process
V124G
-
C-terminus involved in the formation of disulfide bonds during refolding process
V124K
-
C-terminus involved in the formation of disulfide bonds during refolding process
V124L
-
C-terminus involved in the formation of disulfide bonds during refolding process
V124W
-
C-terminus involved in the formation of disulfide bonds during refolding process
V43A
-
substitution of the hydrophobic residue valin 43 by alanin results in an increase in the global stability of the ribonuclease A structure of 4.02 kJ/mol in free energy
V43C/R85C
-
crystallization data. Residues V43 and R85 are not involved in the folding/unfolding transition states ensemble
V43C/R85C
-
site-directed mutagenesis
V47A
-
detailed study on thermodynamic parameters
V47A
-
thermodynamic analysis of pressure-unfolding and kinetics for positive pressure-jumps
V47A
-
site-directed mutagenesis
V54A
-
detailed study on thermodynamic parameters
V54A
-
thermodynamic analysis of pressure-unfolding and kinetics for positive pressure-jumps
V54A
-
site-directed mutagenesis
V57A
-
detailed study on thermodynamic parameters
V57A
-
thermodynamic analysis of pressure-unfolding and kinetics for positive pressure-jumps
V57A
-
site-directed mutagenesis
V63A
-
detailed study on thermodynamic parameters
Y115W
-
large increase in fluorescence yield upon unfolding. Analysis of reversible pressure dependent unfolding profiles. With increasing temperature, the sigmoidal unfolding transition is shifted towards higher pressures
Y115W
-
fluorescent enzyme variant
Y25A
-
critical position for the ribonuclease A stability
Y25F
-
decreases the stability of the enzyme by 7.41 kJ/mol
Y73A
-
a minor role in the stabilization of the protein
Y97A
-
substitution of Tyr97 results in a variant significantly destabilized
Y97L
-
substitution of Tyr97 results in a variant significantly destabilized
D121A
-
Km-value for poly(C) is 2.4fold higher than wild-type value, Km-value for yeast tRNA is 1.25fold higher than wild-type value, turnover-number for poly(C) is 16.5fold lower than wild-type value, turnover-number for yeast tRNA is 1.3fold lower than wild-type value. ASp121 is crucial for the catalytic activity and may be involved in the depolymerization activity of the enzyme
G38D
-
as active as wild type enzyme towards ssRNA, poly(C) and poly(U) single-stranded homopolymers. With 3fold reduction of the dsRNA degrading activity
G38D
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
G38R/R39G/N67R/N88R
-
20% of wild-type activity. Kd value of complex with ribonuclease inibitor 0.032 nM
G89R/S90R
-
PE5 variant
K102A
-
as active as wild type enzyme towards ssRNA, poly(C) and poly(U) single-stranded homopolymers
K62A
-
full catalytic activity, reduced protein stability and DNA unwinding activity
K6A
-
reduced catalytic activity on both ssRNA and dsRNA
N67D/N88A/G89D/R91D
-
76% of wild-type activity. Kd value of complex with ribonuclease inibitor 45 nM
Q28A
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Q28A/G38D
-
site-directed mutagenesis, the mutant shows reduced activity and thermal stability compared to the wild-type enzyme
Q28A/G38D/R39A
-
site-directed mutagenesis, the mutant shows highly reduced activity and thermal stability compared to the wild-type enzyme
Q28A/R39A
-
site-directed mutagenesis, the mutant shows reduced activity and thermal stability compared to the wild-type enzyme
Q28L
-
site-directed mutagenesis, the mutant shows enhanced activity compared to the wild-type enzyme
Q28L/R31C/R32C/N34K/E111G
-
extremely cytotoxic
Q28L/R39A
-
site-directed mutagenesis, the mutant shows reduced activity and thermal stability compared to the wild-type enzyme
Q37R/R39D/K66R/N67G/G68D/G89R/S90G/R91D
-
PI5 variant
R31E/K66R/N67G/G68D/R91A
-
PE3I2 variant
R31E/Q37R/R39D/R91A
-
PE3I1 variant
R31E/R91A
-
PE3 variant
R32A
-
full catalytic activity
R39A
-
site-directed mutagenesis, the mutant shows reduced activity and thermal stability compared to the wild-type enzyme
R39A/G38D
-
site-directed mutagenesis, the mutant shows highly reduced activity and thermal stability compared to the wild-type enzyme
R39D/N67D/G89D/R91D
-
16% of wild-type activity. Kd value of complex with ribonuclease inibitor 1000 nM
R39D/N67D/N88A/G89D
-
24% of wild-type activity. Kd value of complex with ribonuclease inibitor 16 nM
R39D/N67D/N88A/G89D/R91D
-
30% of wild-type activity. Kd value of complex with ribonuclease inibitor 1700 nM
R39D/N67D/N88A/R91D
-
48% of wild-type activity. Kd value of complex with ribonuclease inibitor 278 nM
R39D/N88A/G89D/R91D
-
48% of wild-type activity. Kd value of complex with ribonuclease inibitor 68 nM
R39L/N67L/N88A/G89L/R91L
-
143% of wild-type activity. Kd value of complex with ribonuclease inibitor 30 nM
R4A
-
as active as wild type enzyme towards ssRNA, poly(C) and poly(U) single-stranded homopolymers
R4A/G38D/K102A
-
ADA variant, triple mutant. This variant shows 62% and 83% activity on poly(C) and poly(U), respectively, with respect to wild type enzyme
R4A/K6A/Q9E/D16G/S17N
P07998
more exolytic cleavage preference than parental pancreatic ribonuclease
R4A/K6A/Q9E/D16G/S17N/T36Y/Q37R/G38W
-
29.6% catalytic efficiency of wild type
C87A/C104A
-
66% of wild-type activity, decrease in melting temperature
C87A/C104A
-
66% of wild-type activity, reduced cytotoxic and cytostatic properties, IC50 values for K-562 cells 0.0046 mM
E91A
-
mutant prefers adenine over guanine
E91K
-
1.6-fold preference for UpA over UpG
E91N
-
mutant prefers adenine over guanine
E91Q
-
mutant prefers adenine over guanine
F28A
-
61% of wild-type activity, decrease in melting temperature
F28A
-
61% of wild-type activity, reduced cytotoxic and cytostatic properties, IC50 values for K-562 cells 0.0043 mM
F28T
-
60% of wild-type activity, decrease in melting temperature
F28T
-
60% of wild-type activity, reduced cytotoxic and cytostatic properties, IC50 values for K-562 cells 0.0037 mM
F36A
-
69% of wild-type activity, reduced cytotoxic and cytostatic properties, IC50 values for K-562 cells 0.0039 mM
F36Y
-
80% of wild-type activity, decrease in melting temperature
F36Y
-
80% of wild-type activity, reduced cytotoxic and cytostatic properties, IC50 values for K-562 cells 0.0027 mM
Glp1E
-
41% of wild-type activity, decrease in melting temperature
Glp1E
-
41% of wild-type activity, reduced cytotoxic and cytostatic properties, IC50 values for K-562 cells 0.0099 mM
glp1P
-
44% of wild-type activity, decrease in melting temperature
glp1P
-
44% of wild-type activity, reduced cytotoxic and cytostatic properties, IC50 values for K-562 cells 0.015 mM
T25R/N26W/L27R
-
8.4% catalytic efficiency of wild type
T89D
-
3fold increased in the value of kcat/KM for UpA cleavage
T89N/E91A
-
mutant prefers adenine over guanine 2.6fold, crystallization data of mutant in complex with 5'-AMP
E35L
-
complete loss of ribonuclease activity
F31A
P61991
considerable decrease in stability against heat and pressure. Analysis of thermodynamic parameters
F31A
P61991
loss in thermo and piezostabilities by at least 27 K and 10 kbar. Determination of solution structure by NMR spectroscopy reveals the change in orientation of the W23 side chain, which in the wild type is completely exposed to the solvent, whereas in the mutant is largely buried in the aromatic cluster. Mutation leads to strong distortion in the alpha-sheets with loss in several hydrogen bonds, and increased flexibility of some stretches of the backbone
F31Y
P61991
considerable decrease in stability against heat and pressure. Analysis of thermodynamic parameters
K12L
-
complete loss of ribonuclease activity
M79A
-
a minor role in the stabilization of the protein
additional information
-
A4C/G88R/V118C mutant, with a new disulfide bond that links the N and C termini, is more stable to thermal denaturation than wild type and G88R enzymes. The conformational stability of the C40A/G88R/C95A and C65A/C72A/G88R mutants is less than that of G88R. A4C/C65A/C72A/G88R/V118C mutant, with a new disulfide bond is more stable than C65A/C72A/G88R mutant
additional information
-
cross-linking of enzyme or its covalently linked dimer to polyspermine using dimethyl suberimidate. The in vitro and in vivo cytotoxic activity of treated monomeric enzyme is not higher than that of free polyspermine, but dimeric suberimidate-treated enzyme proves to be a more efficient antitumor agent both in vitro and in vivo
additional information
-
series of mutations in residues V54, V57, I106 and V108 most critical for stability. Detailed study on thermodynamic parameters
additional information
-
use of gene duplication to generate tandem enzymes covalently bound by peptide linker. Tandemization has minor effects on the activity and stability in comparison to monomeric RNase A. Relative activity decreases by 10-50%, and melting temperature decreases by less than 2.5 K. Tandemization results in remarkable cytotoxicity, decreasing the IC50 values with K-562 cells to 0.070-0.013 mM
additional information
P61823
transgenic expression in Nicotiana tabacum as a protection against tobacco mosaic virus. Transgenic plants are characterized by an increased level of enzyme activity in leaf extract and exhibit a significantly higher level of protection against the virus infection than control. Protection is evident by the absence or significant delay of the appearance of typical mosaic symptoms and the retarded accumulation of infectious virus and viral antigen
additional information
-
construction of enzyme dimer composed of monomeric units covalently linked by a single amide bond between the side-chains of residues K66 and E9 by incubation of a lyophilized preparation of enzyme under vacuum at 85C. Procedure does not induce a significant conformational change, dimer shows an 2fold increase in activity over monomeric enzyme and is not inhibited by the cellular ribonuclease inhibitor protein
additional information
-
the structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A is solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations have only minor influence on the global structure of ribonuclease A. The structural changes have individual character that depends on the localization of mutated residue, however, they seem to expand from mutation site to the rest of the structure. Analysis of the difference distance matrices reveal that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation
additional information
-
substitution of P114 with residues that strongly prefer a trans peptide bond, like Ala, Gly, results in significant population of the C-terminal domain-swapped dimer under near-physiological conditions of pH 8.0 and 37C. This is in stark contrast to dimerization of wild-type RNase A, which requires incubation under extreme conditions such as lyophilization from acetic acid or elevated temperature
additional information
-
two RNase A variants, P114G and P93A, have the same global stability yet very different domain-swapping propensity, differences in protection factors suggest differential local dynamics
H110A
Q27J90, Q27J91
complete loss of activity
additional information
Q27J90, Q27J91
substitution of domain I of Gallus gallus rRNase A-1 onto the rRNase A-2 backbone significantly attenuats bactericidal activity. Taken further, substitution of either domain II or III of rRNase A-1 alone, or domains II and III together eliminates the bactericidal activity of RNase A-2; substitution of the RNase A-1 backbone with either domain I, and more so, II, or III of Gallus gallus RNase A-2 confers bactericidal activity on RNase A-1
K74A
-
altered seconday structure, reduced protein stability and DNA unwinding activity, reduced catalytic activity on both ssRNA and dsRNA
additional information
P07998
enzyme variant PM8, in which the sequence of the N-terminal domain has been substituted by that of bovine seminal ribonuclease and Pro101 has been substituted by Glu. At 29C in 20% (v/v) ethanol, a significant portion of PM8 is in dimeric form without formation of higher oligomers. Dissociation constant of this dimer is 5 mM at 29C. A decrease in temperature shifts the monomer-dimer equilibrium to dimer. Model for dimerization with an open interface formed first and then intersubunit interactions stabilize the hinge loop in a conformation that completely displaces the equilibrium between nonswapped and swapped dimers to swapped ones
additional information
-
all RNase A oligomers obtained either by cross-linking reactions or by one of the other ways by which the enzyme protein can aggregate, acquire the ability to degrade double-stranded polyribonucleotides
Renatured/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
4-chlorobutan-1-ol induces reversible thermal transition in ribonuclease A at low concentrations, irreversible at intermediate concentrations (50-250 mM) and again reversible transitions at further higher concentrations of the alcohol (250-400 mM)
-
analysis of conformational changes by picosecond time-resolved fluorescence of the six tyrosine residues. Upon thermal or chemical unfolding only Y25, Y92, and Y76 undergo significant displacement from their nearest -SS- bridge. A single unfolding event around 59C affects all these residues similarly
-
analysis of reversible pressure dependent unfolding profiles of mutant Y115W. With increasing temperature, the sigmoidal unfolding transition is shifted towards higher pressures
-
comparison of folding kinetics with Rana pipiens' onconase and bovine angiogenin at pH 8.0 and 15C. Direct correlation between the number of cis-prolyl bonds in a native protein and the complexity with which it folds via slower phases
-
folding/unfolding kinetics of enzyme with and without a covalent crosslink in the form of a fifth disulfide bond. Residues V43 and R85 are not involved in the folding/unfolding transition states ensemble, and residues A4 and V118 may form non-native contacts
-
photo-CIDNP NMR spectroscopy study for monitoring of the real-time refolding of ribonuclease A following dilution from a high concentration of urea or guanidine-HCl denaturant, two distinct kinetic processes are apparent, a faster step with time constant of 4-8 s (4.2 s in urea and 7.3/7.6 s in guanidine-HCl) and a slower one with time constant 16-24 s (16.6 s in urea and 24.0 s in guanidine-HCl). The latter is attributed to the cis-trans isomerization of Pro 93 and is responsible for the slow disappearance of the signal from Tyr 92 in the folding intermediate observed in the guanidine-HCl experiment
-
protein disulfide isomerase acts both as chaperone and an oxidase during the folding of enzyme. Protein disulfide isomerase catalyzes the conversion of the kinetically trapped enzyme intermediates, des-[26-84] and des-[58-110], by re-shuffling them into the on-pathway intermediate, des-[40-95], and the formation of the native protein
-
refolding of denatured and reduced RNase A with refolding-facilitating media immobilized with three folding machineries, mini-chaperone (a monomeric apical domain consisting of residues 191-345 of GroEL) and two foldases (DsbA and human peptidyl-prolyl cis-trans isomerase) by mimicking oxidative refolding chromatography. For efficient and simple purification and immobilization simultaneously, folding machineries are fused with the positively-charged consecutive 10-arginine tag at their C-terminal. The immobilized folding machineries are fully functional when assayed in a batch mode
-
study on enzyme folding and refolding kinetics using pressure-jump techniques. The structure of the transition state is a relatively uniformly expanded form half-way between the folded and unfoded states. The pressure-folding transition state looks like a collapsed globule with some secondary structure and a weakenend hydrophobic core
-
study on folding/unfolding by pressure-jump-induced relaxation kinetics. Downward pressure jumps result always in single exponential kinetics, while upward jumps are biphasic in the low pressure range and monophasic at higher pressures. Analysis of the activation volume shows a temperature-dependent shift of the unfolding transition state to a larger volume
-
the ribonuclease A equilibrium unfolding in urea and guanidinium chloride solutions proceeds through a formation of intermediates whose compactness, retention of the larger part hydrophobic core, secondary structure, and native-like folding pattern correspond to the wet molten globule state. The urea intermediate is less compact than that in GuCl. The refolding of the protein denatured by GuCl results in the formation of the intermediate which enzyme activity is virtually the same as the activity of the native protein
-
unfolding molecular dynamics simulations of glycosylated and unglycosylated enzyme. Attachment of monomeric N-acetylglucosyamine to residue N34 results in a change of denaturing process. The glycosylated enzyme remains more stable due to preserved non-local interactions
-
comparison of folding kinetics with bovine RNase A and angiogenin at pH 8.0 and 15C. Direct correlation between the number of cis-prolyl bonds in a native protein and the complexity with which it folds via slower phases
-
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
agriculture
P61823
transgenic expression in Nicotiana tabacum as a protection against tobacco mosaic virus. Transgenic plants are characterized by an increased level of enzyme activity in leaf extract and exhibit a significantly higher level of protection against the virus infection than control. Protection is evident by the absence or significant delay of the appearance of typical mosaic symptoms and the retarded accumulation of infectious virus and viral antigen
analysis
-
synthesis of monodispersed RNase A surface-imprinted particles with good magnetic property for practical bioseparation. Use of methyl methacrylate and ethylene glycol dimethacrylate as the functional and cross-linker monomers to produce particles of 700-800 nm diameter imprinted with ribonuclease A and encapsulated with nanosized Fe3O4 particles. Surface-imprinted particles show good selectivity toward the RNase template over control protein
analysis
-
synthesis of molecularly imprinted polymers from the monomers styren and polyethyleneglycol 400 dimethacylate with high rebinding efficiency of RNase A to polymer. Polymers show high selectivity for RNase A and high stability
analysis
-
preparation of polymeric nanoparticles imprinted with RNase A via miniemulsion polymerization using methyl methacrylate and ethylene glycol dimethacrylate. The addition of poly(vinyl alcohol) as a co-surfactant is effective in preserving the protein structural integrity. Imprinted nanoparticles produces by the optimized method show increased target specificity
analysis
-
study on spermidine modulation of enzyme activity via individual RNA plasmon rulers which combine high throughput with high temporal resolution at the single molecule level and are able to retrieve otherwise obscured information about weak structural stabilizations
analysis
-
pressure tuning hole burning experiments using the UV-absorbing tyrosine residues. Ribonuclease A protein stays intact upon cooling to 2 K. Its various tyrosine sites show characteristic features which can be resolved in pressure tuning hole burning spectra. Reducing the sulfur bridges leads to a loss of the individual features, and the sites become alike. The respective compressibility is reduced by more than a factor of 2 and comes close to the value of free tyrosine in solution. Compared to the reduction of the sulfur bridges, the influence of guanidinium hydrochloride on the pressure tuning behavior is less pronounced
biotechnology
-
synthesis of molecularly imprinted polymers from the monomers styren and polyethyleneglycol 400 dimethacylate with high rebinding efficiency of RNase A to polymer. Polymers show high selectivity for RNase A and high stability
medicine
-
cross-linking of enzyme or its covalently linked dimer to polyspermine using dimethyl suberimidate. The in vitro and in vivo cytotoxic activity of treated monomeric enzyme is not higher than that of free polyspermine, but dimeric suberimidate-treated enzyme proves to be a more efficinet antitumor agent both in vitro and in vivo
medicine
-
use of gene duplication to generate tandem enzymes covalently bound by peptide linker. Tandemization has minor effects on the activity and stability in comparison to monomeric RNase A. Relative activity decreases by 10-50%, and melting temperature decreases by less than 2.5 K. Tandemization results in remarkable cytotoxicity, decreasing the IC50 values with K-562 cells to 0.070-0.013 mM
medicine
-
the chemical conjugation of polyethylene glycol to the RNase A C-dimer, and to two trimers, decreases the aspermatogenic activity of the oligomers while increasing their inhibitory activity on the growth of human UB900518 amelanotic melanoma transplanted in athymic nude mice. The conjugated RNase A oligomers are devoid of any embryotoxic activity
pharmacology
-
radical-scavenging effects of the ribonuclease inhibitor CPRI may contribute to its function in the cell protection from peroxidative injuries unrelated to inhibition of RNases
pharmacology
-
inhibitors can be the starting point for the development of compounds that can be used as pharmaceuticals against pathologies associated with ribonuclease A homologues such as human angiogenin, which is implicated in tumor induced neovascularization
medicine
-
RNase 1 from human healthy pancreas contains only neutral glycans, whereas RNase 1 from pancreas cancer cell lines contains sialylated structures. In serum from patients with pancreatic cancer, there is an increase of 40% in core fucosylation in the main sialylated biantennary glycans of RNase 1
analysis
P14626
studies on application to purify ribonuclease from eggs of Rana catesbeiana with an aqueousaqueous polymer phase system by using a small-scale cross-axis coil planet centrifuge
synthesis
-
expression of enzyme in Escherichia coli and Saccharomyces cerevisiae. Recombinant proteins are indistinguishable from the Sulfolobus solfataricus enzyme on the basis of heat stability, pH optimum and RNA digestion pattern as well as NMR analysis, the only exceptions being that residues K4 and K6 are not methylated in the recombinant enzyme