Literature summary for 3.1.1.29 extracted from

Zhang, F.; Song, Y.; Niu, L.; Teng, M.; Li, X.
Crystal structure of Staphylococcus aureus peptidyl-tRNA hydrolase at a 2.25 A resolution (2015), Acta Biochim. Biophys. Sin. (Shanghai), 47, 1005-1010 .

Cloned(Commentary)

Cloned (Comment)	Organism
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)	Staphylococcus aureus

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Staphylococcus aureus

Crystallization (Comment)

Organism

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

Staphylococcus aureus

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
18400	-	recombinant His6-tagged enzyme, gel filtration	Staphylococcus aureus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
peptidyl-tRNA + H2O	Staphylococcus aureus	-	peptide + tRNA	-	?
peptidyl-tRNA + H2O	Staphylococcus aureus NCTC 8325	-	peptide + tRNA	-	?

Organism

Organism	UniProt	Comment	Textmining
Staphylococcus aureus	Q2G0R9	-	-
Staphylococcus aureus NCTC 8325	Q2G0R9	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration	Staphylococcus aureus

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
additional information	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)	Staphylococcus aureus	?	-	?
additional information	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)	Staphylococcus aureus NCTC 8325	?	-	?
peptidyl-tRNA + H2O	-	Staphylococcus aureus	peptide + tRNA	-	?
peptidyl-tRNA + H2O	-	Staphylococcus aureus NCTC 8325	peptide + tRNA	-	?

Subunits

Subunits	Comment	Organism
monomer	1 * 21700, about, sequence calculation, 1 * 24000, recombinant His6-tagged enzyme, SDS-PAGE	Staphylococcus aureus
More	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	Staphylococcus aureus

Synonyms

Synonyms	Comment	Organism
peptidyl-tRNA hydrolase	-	Staphylococcus aureus
PTH	-	Staphylococcus aureus
SaPth	-	Staphylococcus aureus

General Information

General Information	Comment	Organism
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	Staphylococcus aureus