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Information on EC 3.1.1.29 - aminoacyl-tRNA hydrolase and Organism(s) Staphylococcus aureus and UniProt Accession Q6YP15
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3.1.1.29 aminoacyl-tRNA hydrolaseSpecify your search results
Word Map
- 3.1.1.29
- peptidyl-trnas
- aminoacyl-trnas
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drop-off
- trnalys
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infantile-onset
- drug development
The taxonomic range for the selected organisms is: Staphylococcus aureus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
peptidyl-trna hydrolase, ankzf1, ptrhd1, spovc, mspth, bacterial peptidyl-trna hydrolase, yhr189w, peptidyl-trna hydrolase 2, abpth, mj0051, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
aminoacyl-transfer ribonucleate hydrolase
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hydrolase, aminoacyl-transfer ribonucleate
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N-substituted aminoacyl transfer RNA hydrolase
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peptidyl-tRNA hydrolase
PTH
peptidyl-tRNA hydrolase
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PTH
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of carboxylic ester
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
aminoacyl-tRNA aminoacylhydrolase
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CAS REGISTRY NUMBER
COMMENTARY
9054-98-2
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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
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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additional information
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substrate-binding cleft pattern of SaPth, the cleft is conservatively composed of three segments, namely, a base loop (Gly106-Gly113 in SaPth), a gate loop (Leu89-Val100 in SaPth), and a lid loop (Gly134-Gln148 in SaPth). The base loop constitutes one side of the cleft, and the gate loop and lid loop form the other side of the cleft. A structural comparison among all of the substrate-free structures in Pths reveals three different states of substrate-binding clefts; one state is the closed state (the substrate-binding cleft is closed at both the lid and gate loops, such as in SpPth), the second is the semi-closure state (the substrate-binding cleft is closed at the gate loop but wide-open at the lid loop, such as in MtPth and MsPth), and the third is the open state (the substrate-binding cleft is wide-open when both the lid and gate loops are away from the base loop)
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additional information
?
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substrate-binding cleft pattern of SaPth, the cleft is conservatively composed of three segments, namely, a base loop (Gly106-Gly113 in SaPth), a gate loop (Leu89-Val100 in SaPth), and a lid loop (Gly134-Gln148 in SaPth). The base loop constitutes one side of the cleft, and the gate loop and lid loop form the other side of the cleft. A structural comparison among all of the substrate-free structures in Pths reveals three different states of substrate-binding clefts; one state is the closed state (the substrate-binding cleft is closed at both the lid and gate loops, such as in SpPth), the second is the semi-closure state (the substrate-binding cleft is closed at the gate loop but wide-open at the lid loop, such as in MtPth and MsPth), and the third is the open state (the substrate-binding cleft is wide-open when both the lid and gate loops are away from the base loop)
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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
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8.5
approx. 38% at pH 6.0, approx. 20% of maximal activity at pH 8.5
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
peptidyl-tRNA hydrolase (Pth) catalyzes the release of tRNA to relieve peptidyl-tRNA accumulation. The enzyme activity is essential for the viability of bacteria
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
1 * 21700, about, sequence calculation, 1 * 24000, recombinant His6-tagged enzyme, SDS-PAGE
additional information
additional information
enzyme SaPth was a monomer in solution, the dimerization of SaPth in the crystal may be related to the crystal-packing environment. Four parallel beta-strands (beta1, beta4, beta5, and beta7) form a twisted beta-sheet in the center of the molecule, two beta-strands (beta2 and beta3) are antiparallel to the beta-sheet and are located at one side of the center beta-sheet, and the third antiparallel beta-strand (beta6) is located at the other side. The beta-structure is surrounded at both sides by helices, overview
additional information
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enzyme SaPth was a monomer in solution, the dimerization of SaPth in the crystal may be related to the crystal-packing environment. Four parallel beta-strands (beta1, beta4, beta5, and beta7) form a twisted beta-sheet in the center of the molecule, two beta-strands (beta2 and beta3) are antiparallel to the beta-sheet and are located at one side of the center beta-sheet, and the third antiparallel beta-strand (beta6) is located at the other side. The beta-structure is surrounded at both sides by helices, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His6-tagged enzyme, hanging drop vapor diffusion method, mixing of 2 mg/ml protein in 20 mM Tris-HCl, pH 8.5, and 200 mM NaC with reservoir solution containing 25% PEG 3350, 0.2 M ammonium sulfate, and 0.1 M HEPES, pH 7.5, in a 1:1 ratio, at 16°C for 3 days, X-ray diffraction structure determination and analysis at 2.25 A resolution, molecular replacement using the structure of Pth from Mycobacterium tuberculosis (PDB ID 2Z2I) as the search model
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene pth, DNA and amino acid sequence determination and analysis, molecular phylogenetic analysis, recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Bonin, P.D.; Choi, G.H.; Trepod, C.M.; Mott, J.E.; Lyle, S.B.; Cialdella, J.I.; Sarver, R.W.; Marshall, V.P.; Erickson, L.A.
Expression, purification, and characterization of peptidyl-tRNA hydrolase from Staphylococcus aureus
Protein Expr. Purif.
24
123-130
2002
Staphylococcus aureus (Q6YP15), Staphylococcus aureus
Zhang, F.; Song, Y.; Niu, L.; Teng, M.; Li, X.
Crystal structure of Staphylococcus aureus peptidyl-tRNA hydrolase at a 2.25 A resolution
Acta Biochim. Biophys. Sin. (Shanghai)
47
1005-1010
2015
Staphylococcus aureus (Q2G0R9), Staphylococcus aureus, Staphylococcus aureus NCTC 8325 (Q2G0R9)
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Release 2023.1 (January 2023)
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