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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   M. Selvaraj, S. Roy, N. S. Singh, R. Sangeetha, U. Varshney, M. Vijayan

Date :   22 May 07 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

Chains :   Asym./Biol. Unit : A

Keywords :   Protein Synthesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Selvaraj, S. Roy, N. S. Singh, R. Sangeetha, U. Varshney, M. Vijayan
Structural Plasticity And Enzyme Action: Crystal Structures Of Mycobacterium Tuberculosis Peptidyl-Trna Hydrolase
J. Mol. Biol. V. 372 186 2007
PubMed-ID: 17619020 | Reference-DOI: 10.1016/J.JMB.2007.06.053

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
	Chains	:	A
	EC Number	:	3.1.1.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PRSETBMTUPTH
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RV1014C, PTH
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	PTH

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2Z2I)

(no "Site" information available for 2Z2I)

(no "SS Bond" information available for 2Z2I)

(no "Cis Peptide Bond" information available for 2Z2I)

(no "SAP(SNP)/Variant" information available for 2Z2I)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPT_TRNA_HYDROL_1	PS01195	Peptidyl-tRNA hydrolase signature 1.	PTH_MYCTO	17-30	1	A:17-30
1	PEPT_TRNA_HYDROL_1	PS01195	Peptidyl-tRNA hydrolase signature 1.	PTH_MYCTU	17-30	1	A:17-30
2	PEPT_TRNA_HYDROL_2	PS01196	Peptidyl-tRNA hydrolase signature 2.	PTH_MYCTO	111-121	1	A:111-121
2	PEPT_TRNA_HYDROL_2	PS01196	Peptidyl-tRNA hydrolase signature 2.	PTH_MYCTU	111-121	1	A:111-121

(no "Exon" information available for 2Z2I)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:179
 aligned with PTH_MYCTO | P9WHN6 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
            PTH_MYCTO     1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQ 179
               SCOP domains d2z2ia_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains 2z2iA00 A:1-179  [code=3.40.50.1470, no name defined]                                                                                                                               CATH domains
               Pfam domains -----Pept_tRNA_hydro-2z2iA01 A:6-179                                                                                                                                                Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhhhhhhhhhh....ee......eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhhh....eeeeee........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PEPT_TRNA_HYDR----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------PEPT_TRNA_H---------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z2i A   1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQ 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain A from PDB  Type:PROTEIN  Length:179
 aligned with PTH_MYCTU | P9WHN7 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
            PTH_MYCTU     1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQ 179
               SCOP domains d2z2ia_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains 2z2iA00 A:1-179  [code=3.40.50.1470, no name defined]                                                                                                                               CATH domains
               Pfam domains -----Pept_tRNA_hydro-2z2iA01 A:6-179                                                                                                                                                Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhhhhhhhhhh....ee......eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhhh....eeeeee........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------PEPT_TRNA_HYDR----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------PEPT_TRNA_H---------------------------------------------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z2i A   1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQ 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Peptidyl-tRNA hydrolase-like (33)

Family: automated matches (29)

Protein domain: automated matches (29)

Mycobacterium tuberculosis [TaxId: 83332] (7)

d2z2ia_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1470, no name defined] (8)

Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. (3)

2z2iA00

A:1-179

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Pept_tRNA_hydro] (10)

Family: Pept_tRNA_hydro (10)

Mycobacterium tuberculosis (3)

Pept_tRNA_hydro-2z2iA01

A:6-179

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PTH_MYCTO | P9WHN6)

molecular function
	GO:0004045	aminoacyl-tRNA hydrolase activity	Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (PTH_MYCTU | P9WHN7)

molecular function
	GO:0004045	aminoacyl-tRNA hydrolase activity	Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	PTH_MYCTO \| P9WHN6
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	PTH_MYCTU \| P9WHN7
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	3.1.1.29
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	PTH_MYCTO \| P9WHN6
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UniProtKB/Swiss-Prot
	PTH_MYCTO \| P9WHN6	:	2jrc 2z2j 2z2k 3tck 3tcn 3td2 3td6
	PTH_MYCTU \| P9WHN7	:	2jrc 2z2j 2z2k 3tck 3tcn 3td2 3td6

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SCOP Domains (1, 1)

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