Information on EC 3.1.27.4 - ribonuclease U2

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY
3.1.27.4
-
RECOMMENDED NAME
GeneOntology No.
ribonuclease U2
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Ap or Gp with 2',3'-cyclic phosphate intermediates
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
hydrolysis of phosphoric ester
-
-
hydrolysis of phosphoric ester
Ustilago sphaerogena CBS 534.71
-
-
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Pleospora RNase
-
-
-
-
Purine specific endoribonuclease
-
-
-
-
Purine-specific ribonuclease
-
-
-
-
Purine-specific RNase
-
-
-
-
Ribonuclease (purine)
-
-
-
-
ribonuclease U2
P00654
-
ribonuclease U2A
P00654
-
ribonuclease U2B
P00654
-
Ribonuclease U3
-
-
-
-
RNase U2
-
-
-
-
RNase U2
Ustilago sphaerogena CBS 534.71
P00654
-
-
RNase U2A
P00654
-
RNase U3
-
-
-
-
Trichoderma koningi RNase III
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
37205-57-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
Schizosaccharomyces pombe GP969
-
-
-
Manually annotated by BRENDA team
ATCC 12421 and CBS 534.71
SwissProt
Manually annotated by BRENDA team
CBS 534.71
SwissProt
Manually annotated by BRENDA team
Ustilago sphaerogena CBS 534.71
CBS 534.71
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
physiological function
-
the endonuclease cleavage of many small nuclear RNAs is equally important in terminating the transcription of the U2 snRNA in Schizosaccharomyces pombe. Reversed torpedoes model for the termination and maturation of the U2 snRNA, the Pac1 endonuclease cleavage provides entry sites for the 3' and 5' exonuclease activities, leading to RNA maturation in one direction and transcript termination in the other
physiological function
Schizosaccharomyces pombe GP969
-
the endonuclease cleavage of many small nuclear RNAs is equally important in terminating the transcription of the U2 snRNA in Schizosaccharomyces pombe. Reversed torpedoes model for the termination and maturation of the U2 snRNA, the Pac1 endonuclease cleavage provides entry sites for the 3' and 5' exonuclease activities, leading to RNA maturation in one direction and transcript termination in the other
-
additional information
-
mechanism of isoaspartate formation within the Asp45-Glu46 sequence of ribonuclease U2, overview. In the succinimide-formation reaction water 219 receives a proton from the N atom of Glu46 as a general base and waters 190 and 220 stabilize the tetrahedral intermediate, and in the succinimide-hydrolysis reaction water 219 provides a proton for the N atom of Glu46 as a general acid
additional information
-
formation of isoAsp32 induces a single turn unfolding of the alpha-helix from Asp29 to Asp34, and the region from Asp29 to Arg35 forms a U-shaped loop structure, overview. IsoAsp32 protrudes from the surface of the protein, and the abnormal beta-peptide bond in the main-chain and alpha-carboxylate in the side-chain is fully exposed. The structure suggests that the deamidation of the Asn and the isoAsp formation in proteins could confer immunogenicity
additional information
-
cleavage in the U3 snoRNA transcripts of Schizosaccharomyces pombe can induce transcript termination, the degree of cleavage correlates closely with both RNA maturation and transcript termination. the RNase III-like endonuclease, Pac1, and the nuclear 50-exonuclease, Dhp1p, are essential for RNA production and transcript termination, supporting a ‘reversed torpedoes model in which the endonuclease cut allows 5'- and 3'-exonuclease activities access to the transcript, leading simultaneously to transcript termination in one direction and RNA maturation in the other
additional information
-
Asn32 of RNase U2A rapidly deaminates and isomerizes in alkaline conditions, conformational mechanism, overview. In solution, the region around Asn32-Gly33 is likely to be in equilibrium between multiple conformers with deamination of Asn32 proceeding when the region adopts an extended conformation
additional information
Schizosaccharomyces pombe GP969
-
cleavage in the U3 snoRNA transcripts of Schizosaccharomyces pombe can induce transcript termination, the degree of cleavage correlates closely with both RNA maturation and transcript termination. the RNase III-like endonuclease, Pac1, and the nuclear 50-exonuclease, Dhp1p, are essential for RNA production and transcript termination, supporting a ‘reversed torpedoes model in which the endonuclease cut allows 5'- and 3'-exonuclease activities access to the transcript, leading simultaneously to transcript termination in one direction and RNA maturation in the other
-
SUBSTRATE
PRODUCT                      
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 + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
P00654
-
-
-
?
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
-
r, preferential cleavage at Ap or Gp
-
-
RNA + H2O
3'-Phosphomononucleotides + 3'-phosphooligonucleotides + 2',3'-cyclic nucleotide phosphates
show the reaction diagram
Ustilago sphaerogena CBS 534.71
P00654
-
-
-
?
5'-(U)6-GA-(U)5-3' RNA + H2O
?
show the reaction diagram
-
digestion of the platinated 5'-(U)6-GA-(U)5-3' RNA shows a reaction product corresponding to [UUUUUUGA + Pt(NH3)2 + H],+ depicting RNase cleavage 3' to an adenosine predicted to be involved in a cisplatin diadduct. The platinated G*A* RNA adduct is uniquely recognized and processed by RNase U2, whereas other purine-Pt(II) adducts are not. The basis for this selectivity may arise from the RNase's known A - G preference, allowing the endonuclease in some cases to partially recognize the 3' platinated A despite platinum modification
-
-
?
additional information
?
-
-
YoeB toxin has in vitro Rnase activity that preferentially cleaves at the 3’-end of purine ribonucleotides
-
-
-
additional information
?
-
-
specifically recognizes purine ribonucleotides and catalyzes cleavage of the 3' phosphodiester bond attached to a G or an A. For platinated sequences containing XY = GG, AG, and GU, RNase U2 cleavage is not observed, being blocked at the purine nucleotides predicted to be involved in platinum binding
-
-
-
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
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ca2+
-
region Asp29-Asp37 winds around a calcium ion
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.2
-
RNA
P00654
37°C, pH 4.5, recombinant enzyme
0.23
-
RNA
P00654
37°C, pH 4.5, fungal enzyme
additional information
-
additional information
-
trinucleotides, synthetic substrates
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0852
-
adenosine 3'-(1-naphthyl phosphate)
-
-
0.00983
-
adenosine 3'-(benzyl phosphate)
-
-
0.00317
-
adenosine 3'-(methyl phosphate)
-
-
59.5
-
CpApGp
-
-
14.8
-
UpApGp
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
P00654
specific activity increases 78fold after purification from crude extracts
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4
4.5
-
adenosine 2',3'-cyclic phosphate + uridine
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4.7
4.8
P00654
-
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
10000
-
-
Ustilago sphaerogena, amino acid analysis
12400
-
-
Ustilago sphaerogena, sedimentation equilibrium
12490
-
P00654
-
12590
-
-
mutant C1S/C54S, MALDI-TOF
13030
-
-
wild type, MALDI-TOF
13330
-
-
mutant H101Q, MALDI-TOF, posttranslational modification suggested
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 11000, SDS-PAGE of nonreduced protein, x * 22000, SDS-PAGE of reduced protein
additional information
-
protein does not bind SDS under SDS-PAGE conditions. Electrophoretic mobility of the nonreduced protein roughly corresponds to its molecular mass, while migration of the reduced protein would be in accordance with the expected molecular mass of the dimer
additional information
-
formation of isoAsp32 induces a single turn unfolding of the alpha-helix from Asp29 to Asp34, and the region from Asp29 to Arg35 forms a U-shaped loop structure, overview
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
heterotrimeric complex of (YefM)2-YoeB antitoxin-toxin pair and free YoeB structure. Conformational rearrangement of YoeB RNase catalytic site upon binding of YefM
-
isoAsp containing ribonuclease U2B, hanging drop vapor diffusion method, 0.004 ml of 10 mg/ml protein in 50 mM sodium citrate, pH 4.5, containing 50 mM sodium chloride, are mixed with 0.004 ml of reservoir solution containing 0.84 M sodium dihydrogen phosphate and 1.26 M dipotassium hydrogen phosphate, pH 6.9, equilibration against 0.4 ml reservoir solution, 20°C, 2 days, X-ray diffraction structure determination and analysis at 1.32 A resolution
-
ribonuclease U2 complexed with adenosine 3'-monophosphate, hanging drop vapour diffusion method, 0.005 ml of protein solution containing 20 mg/ml RNase U2A and 8 mM adenosine 3'-monophosphate, pH 4.5, is mixed with 0.005 ml of reservoir solution containing 12.5% w/w PEG 8000, 200 mM calcium acetate, 100 mM sodium cacodylate, pH 3.75, 12.5% w/w PEG 8000, equilibration against 0.4 ml reservoir solution, 20°C, 3 days, X-ray diffraction structure determination and analysis at 0.96-0.99 A resolution
-
RNase U2A in complex with 2'-adenylic acid and Ca2+ ions, X-ray diffraction structure determination and analysis at 1.03 A resolution
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
80
-
-
unstable above
100
-
-
unstable above
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
3 Months, 0-4°C
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
native RNase U2A by anion-exchange and 5'-adenylate aminohexyl affinity chromatography
-
purification of recombinant enzyme using several chromatographic steps, including affinity chromatography on 2´-5'-ADP-Sepharose
P00654
purification of recombinant enzyme using several chromatographic steps, including DEAE-cellulose and affinity chromatography on 2'-5'-ADP-Sepharose
P00654
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Pac1 endonuclease cleavage is required for U3 snoRNA gene transcription termination and RNA maturation, the degree of cleavage correlates closely with both RNA maturation and transcript termination. U3B snoRNA gene expression system containing a tagged Schizosaccharomyces pombe snU32 locus expressed under its own promoter and the dominant plasmid-derived U3B snoRNA
-
expressed in Pichia pastoris, different signal-peptide cleavage processing sites for different recombinant proteins
-
expression in Escherichia coli and Pichia pastoris
P00654
expression in Pichia pastoris
P00654
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
H83Q
-
no enzymic activity
R65A
-
no enzymic activity
Y84A
-
no enzymic activity
Y84F
-
reduced enzymic activity
C1S/C54S
-
lacking one disulfide bridge, 60% of wild-type activity
H101Q
-
devoid of detectable activity