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Information on EC 2.7.7.56 - tRNA nucleotidyltransferase
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EC Tree
2.7.7.56 tRNA nucleotidyltransferaseIUBMB Comments
Brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in Escherichia coli by a phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate. Not identical with EC 2.7.7.8 polyribonucleotide nucleotidyltransferase.
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Word Map
- 2.7.7.56
- polynucleotide
- exoribonuclease
- pnpases
-
exosome
-
phosphorolytic
-
cca-adding
- aminoacylation
-
exonucleolytic
- 3'-terminus
-
2.7.7.25
-
pyre
- trnaphe
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
trna nucleotidyltransferase, rnase ph, rph-1, ribonuclease ph, rnase ph ring, phosphate-dependent exonuclease, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
nuclease, ribo-, PH
-
-
-
-
phosphate-dependent exonuclease
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-
-
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ribonuclease PH
-
-
-
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RNase PH
RNase PH
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-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
tRNAn+1 + phosphate = tRNAn + a nucleoside diphosphate
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
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-
-
-
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PATHWAY SOURCE
PATHWAYS
-
-
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SYSTEMATIC NAME
IUBMB Comments
tRNA:phosphate nucleotidyltransferase
Brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in Escherichia coli by a phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate. Not identical with EC 2.7.7.8 polyribonucleotide nucleotidyltransferase.
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CAS REGISTRY NUMBER
COMMENTARY
116412-36-3
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
poly(A) + phosphate
?
-
phosphorolysis of poly(A) 15times more rapidly than of tRNA-C-C-A-Cn
-
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
substrate specificity
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
dependent on phosphate
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
dependent on phosphate
enzyme can utilize all dinucleotides as substrates for the reverse reaction
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
phosphorolysis of poly(A) 15times more rapidly than of tRNA-C-C-A-Cn
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
tRNA-C-C-A-Cn
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
tRNA-C-C-A-Cn
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
reverse reaction is synthetic
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ir
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in E. coli by phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in E. coli by phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in E. coli by phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
implicated in the 3'-processing of tRNA precursors
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ir
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
implicated in the 3'-processing of tRNA precursors
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
role in tRNA processing and RNA degradation
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
implicated in the 3'-processing of tRNA precursors
-
r
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
involved in the maturation of tRNA precursors and especially important for removal of nucleotide residues near the CCA acceptor end of the mature tRNAs
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-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors, degradation of the last few nucleotides before the acceptor stem
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-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
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degradation of 16S rRNA substrate 3' end
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-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
the enzyme is a 3' to 5' RNase. The enzyme digests through RNA duplexes of moderate stability
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
16S rRNA substrate
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-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
the enzyme is a 3' to 5' RNase. RNase PH uses phosphate as a nucleophile to catalyze RNA cleavage
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
the enzyme is a 3' to 5' RNase. The enzyme digests through RNA duplexes of moderate stability
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
the enzyme is a 3' to 5' RNase. RNase PH uses phosphate as a nucleophile to catalyze RNA cleavage
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
degradation of 16S rRNA substrate 3' end
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
16S rRNA substrate
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
catalyzes the removal of nucleotides at the 3' end of the tRNA precursor, leading to the release of nucleoside diphosphate, and generates the CCA end during the maturation process
-
-
?
additional information
?
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-
phosphate-dependent tRNA nucleotidyltransferase and polynucleotide phosphorylase activity play an essential role that affects ribosome metabolism, this function cannot be taken over by any of the hydrolytic exonucleases present in the cell
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-
?
additional information
?
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for 16S rRNA degradation during glucose starvation, leading to slow cell growth, begins with shortening of its 3' end in a reaction catalyzed by RNase PH
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-
?
additional information
?
-
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for 16S rRNA degradation during glucose starvation, leading to slow cell growth, begins with shortening of its 3' end in a reaction catalyzed by RNase PH
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-
?
additional information
?
-
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the reaction proceeds via strongly bound phosphate ions in the phosphorolytic active sites of mthRrp41 protein
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-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
reverse reaction is synthetic
-
ir
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in E. coli by phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in E. coli by phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
brings about the final exonucleolytic trimming of the 3'-terminus of tRNA precursors in E. coli by phosphorolysis, producing a mature 3'-terminus on tRNA and nucleoside diphosphate
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
implicated in the 3'-processing of tRNA precursors
-
ir
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
implicated in the 3'-processing of tRNA precursors
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
role in tRNA processing and RNA degradation
-
r
tRNAn+1 + phosphate
tRNA + a nucleoside diphosphate
-
implicated in the 3'-processing of tRNA precursors
-
r
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
involved in the maturation of tRNA precursors and especially important for removal of nucleotide residues near the CCA acceptor end of the mature tRNAs
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors, degradation of the last few nucleotides before the acceptor stem
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
degradation of 16S rRNA substrate 3' end
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
the enzyme is a 3' to 5' RNase. The enzyme digests through RNA duplexes of moderate stability
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
the enzyme is a 3' to 5' RNase. The enzyme digests through RNA duplexes of moderate stability
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
degradation of 16S rRNA substrate 3' end
-
-
?
tRNAn+1 + phosphate
tRNAn + a nucleoside diphosphate
-
catalyzes the removal of nucleotides at the 3' end of the tRNA precursor, leading to the release of nucleoside diphosphate, and generates the CCA end during the maturation process
-
-
?
additional information
?
-
-
phosphate-dependent tRNA nucleotidyltransferase and polynucleotide phosphorylase activity play an essential role that affects ribosome metabolism, this function cannot be taken over by any of the hydrolytic exonucleases present in the cell
-
-
?
additional information
?
-
-
for 16S rRNA degradation during glucose starvation, leading to slow cell growth, begins with shortening of its 3' end in a reaction catalyzed by RNase PH
-
-
?
additional information
?
-
-
for 16S rRNA degradation during glucose starvation, leading to slow cell growth, begins with shortening of its 3' end in a reaction catalyzed by RNase PH
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
KCl
Mg2+
Mn2+
additional information
Co2+
-
30% of the activity with Mg2+, 2 mM somewhat more effective than 5 mM
Mn2+
-
40% of the activity with Mg2+, 2 mM somewhat more effective than 5 mM
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
the enzyme appears to be sensitive to the CCA motif and is surprisingly slow to remove the last nucleotide to generate the functional tRNA
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Anemia, Sideroblastic
In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity.
Carcinoma, Ehrlich Tumor
Effect of nucleoside 5'-triphosphates on tRNA nucleotidyltransferase activity in cytoplasmic fractions of various types of mammalian cells.
Carcinoma, Ehrlich Tumor
Possible regulation by nucleosidediphosphate kinase involvement of the synthesis of tRNA 3'-terminal -pCpCpA in mammalian cells.
Infections
A physiological role for tRNA nucleotidyltransferase during bacteriophage infection.
Melanoma
Defining the domains of human polynucleotide phosphorylase (hPNPaseOLD-35) mediating cellular senescence.
Neoplasms
A unique T-cell monoclonal antibody with potential uses in autologous bone marrow transplantation.
Neoplasms
Effect of nucleoside 5'-triphosphates on tRNA nucleotidyltransferase activity in cytoplasmic fractions of various types of mammalian cells.
Neoplasms
Identification of a tRNA nucleotidyltransferase and its substrates in virions of avian RNA tumor viruses.
Neoplasms
Possible regulation by nucleosidediphosphate kinase involvement of the synthesis of tRNA 3'-terminal -pCpCpA in mammalian cells.
Retinitis Pigmentosa
In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity.
Starvation
Degradation of ribosomal RNA during starvation: comparison to quality control during steady-state growth and a role for RNase PH.
Starvation
Elucidation of pathways of ribosomal RNA degradation: an essential role for RNase E.
Starvation
Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression.
Starvation
RNase II regulates RNase PH and is essential for cell survival during starvation and stationary phase.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
full-length protein with translational start at ATG1 (Met1) and two splice variants with translational start at ATG2 (Met6) and ATG3 (Met69)
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brenda
enzyme mutant deficient in tRNA nucleotidyltransferase and polynucleotide phosphorylase activity
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brenda
naturally acquired truncated inactive ribonuclease PH variant
UniProt
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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the core of the exosome is a versatile multisubunit RNA processing enzyme found in archaea and eukaryotes, which includes a ring of six RNase PH subunits
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brenda
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partial localisation of full-length protein and isoform with translational start at ATG2 (Met6), targeting dependent not only on N-terminal 68 amino acids
brenda
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partial localisation of full-length protein and isoform with translational start at ATG2 (Met6), targeting dependent not only on N-terminal 68 amino acids
brenda
-
localisation of isoform with translational start at ATG3 (Met69), lacking N-terminal 68 residues
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
additional information
-
the core of the exosome is a versatile multisubunit RNA processing enzyme found in archaea and eukaryotes, which includes a ring of six RNase PH subunits, all six RNase PH monomers are catalytically active in the homohexameric RNase PH. Modeling of the Mth exosome RNase PH ring, overview
malfunction
-
absence of RNase PH and polynucleotide phosphorylase, EC 2.7.7.8, causes growth defects. Absence of both enzymes results in the appearance and accumulation of novel mRNA degradation fragments, which are also observed in strains containing mutations in RNase R and PNPase, enzymes whose collective absence is known to cause an accumulation of structured RNA fragments. Single or double deletion of either pnp or rph had a moderate effect on the rpsO, trxA, or lpp mRNAs
malfunction
-
in the absence of RNase PH, there is no 3' end trimming of 16S rRNA and no accumulation of rRNA fragments, and total RNA degradation is greatly reduced. In contrast, the degradation pattern in quality control remains unchanged when RNase PH is absent
malfunction
-
absence of RNase PH and polynucleotide phosphorylase, EC 2.7.7.8, causes growth defects. Absence of both enzymes results in the appearance and accumulation of novel mRNA degradation fragments, which are also observed in strains containing mutations in RNase R and PNPase, enzymes whose collective absence is known to cause an accumulation of structured RNA fragments. Single or double deletion of either pnp or rph had a moderate effect on the rpsO, trxA, or lpp mRNAs
-
malfunction
-
in the absence of RNase PH, there is no 3' end trimming of 16S rRNA and no accumulation of rRNA fragments, and total RNA degradation is greatly reduced. In contrast, the degradation pattern in quality control remains unchanged when RNase PH is absent
-
metabolism
-
RNase PH is involved in the starvation rRNA degradative pathway
metabolism
-
RNase PH is involved in the starvation rRNA degradative pathway
-
physiological function
-
role for RNase PH in the degradation of structured RNA, overview
physiological function
-
the enzym eis required for the pathway of ribosomal RNA degradation during glucose starvation, not for the pathway of ribosomal RNA degradation in quality control during steady-state growth
physiological function
during ribosome degradation in starving cells, RNase II regulates the amount of RNase PH present, via RNase PH stability. RNase PH normally decreases as much as 90% during starvation, in the absence of RNase II the amount of RNase PH remains relatively unchanged. In the presence of RNase II, nutrient deprivation leads to a dramatic reduction in the amount of RNase PH, thereby limiting the extent of rRNA degradation and ensuring cell survival. In the absence of RNase II, RNase PH levels remain high, leading to excessive ribosome loss and ultimately to cell death
physiological function
laboratory strains MG1655 and W3110 have naturally acquired the Rph-1 allele, encoding a truncated catalytically inactive RNase PH protein. Rph-1 protein inhibits RNase P-mediated 5'-end maturation of primary pre-tRNAs with leaders of less than 5 nucleotides in the absence of RppH, an RNA diphosphohydrolase. RppH is not required for 5'-end maturation of endonucleolytically generated pre-tRNAs in the Rph-1 strain and for any tRNAs in Rph mutant or Rp+x03 strains
physiological function
polynucleotide phosphorylase and RNase PH interact to support sRNA stability, activity, and base pairing in exponential and stationary growth conditions. They facilitate the stability and regulatory function of the sRNAs RyhB, CyaR, and MicA during exponential growth. Polynucleotide phosphorylase may contribute to pairing between RyhB and its mRNA targets. During stationary growth, each sRNA responds differently to the absence or presence of PNPase and RNase PH. Polynucleotide phosphorylase and RNase PH stabilize only Hfq-bound sRNAs
physiological function
-
role for RNase PH in the degradation of structured RNA, overview
-
physiological function
-
the enzym eis required for the pathway of ribosomal RNA degradation during glucose starvation, not for the pathway of ribosomal RNA degradation in quality control during steady-state growth
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hexamer
-
multisubunit RNA processing enzyme including a ring of six RNase PH subunits
additional information
additional information
-
enzyme mutant deficient in tRNA nucleotidyltransferase and polynucleotide phosphorylase activity shows differing ribosome structure, the 50S subunit is reduced, the 23S subunit is degraded
additional information
-
the 1.9 A crystal structures of the apo and the phosphate-bound forms of RNase PH from reveal a monomeric RNase PH with an alpha/beta-fold tightly associated into a hexameric ring structure in the form of a trimer of dimers
additional information
-
structure elements of RNase pH-like proteins
additional information
-
structure elements of RNase pH-like proteins
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop vapour diffusion method, wild-type and triple mutant R68Q-R73Q-R76Q RNase PH crystallized and the structures determined by X-ray diffraction to medium resolution. Wild-type and triple mutant RNase PH crystallize as a hexamer and dimer, respectively
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purified recombinant mthRrp41-mthRrp42 protein complex, hanging-drop vapour diffusion, 0.001 ml of protein in 25 mM Tris pH 7.5, 0.15 M NaCl, mixed with 0.001 ml of reservoir solution containing 5% 2-propanol, 20% PEG 3350, and 0.1 M succinic acid pH 7.0, X-ray diffraction structure determination and analysis at 2.65 A resolution
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hanging-drop vapor diffusion method. The 1.9 A crystal structures of the apo and the phosphate-bound forms of RNase PH from reveal a monomeric RNase PH with an alpha/beta-fold tightly associated into a hexameric ring structure in the form of a trimer of dimers
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
R68Q-R73Q-R76Q
-
triple mutant RNase PH crystallize as a dimer, compared to wild-type enzyme that crystallizes as a hexamer
R69S/R77S
-
mutation leads to the dissociation of RNase PH hexamer into dimers without perturbing the overall monomeric structure
R74S
-
mutation leads to the dissociation of RNase PH hexamer into dimers without perturbing the overall monomeric structure
R74S/R77S
-
mutation leads to the dissociation of RNase PH hexamer into dimers without perturbing the overall monomeric structure
additional information
-
enzyme mutant deficient in tRNA nucleotidyltransferase and polynucleotide phosphorylase activity grows slowly at 37°C, shows a dramatically reduced tRNATyrsu3+ suppressor activity, displays reversible cold-sensitivity, and performs normal tRNA synthesis, ribosome structure and function are severely affected, particularly at lower temperatures of 31°C and below
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
45
additional information
-
enzyme mutant deficient in tRNA nucleotidyltransferase and polynucleotide phosphorylase activity displays reversible cold-sensitivity, ribosome structure and function are severely affected, particularly at lower temperatures of 31°C and below
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged mthRrp41-mthRrp42 protein complex from Escherichi coli strain E2566 by nickel affinity chromatography and ultrafiltration
-