3TD2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM TUBERCULOSIS - FORM 5

Authors :   M. Selvaraj, R. Ahmad, U. Varshney, M. Vijayan

Date :   10 Aug 11 (Deposition) - 15 Feb 12 (Release) - 15 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Pth, Hydrolysis Of Peptidyl-Trna, Peptidyl-Trna, Cytosol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Selvaraj, R. Ahmad, U. Varshney, M. Vijayan
Structures Of New Crystal Forms Of Mycobacterium Tuberculosis Peptidyl-Trna Hydrolase And Functionally Important Plasticity Of The Molecule
Acta Crystallogr. , Sect. F V. 68 124 2012
PubMed-ID: 22297982 | Reference-DOI: 10.1107/S1744309111052341

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
	Chains	:	A
	EC Number	:	3.1.1.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSETBMTUPTH
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MT1042, MTCY10G2.35, PTH, RV1014C
	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 3TD2)

(no "Site" information available for 3TD2)

(no "SS Bond" information available for 3TD2)

(no "Cis Peptide Bond" information available for 3TD2)

(no "SAP(SNP)/Variant" information available for 3TD2)

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 3TD2)

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:187
 aligned with PTH_MYCTO | P9WHN6 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
            PTH_MYCTO     1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPAQNR 187
               SCOP domains d3td2a_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhhhh....ee......eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhhh....eeeeee........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PEPT_TRNA_HYDR------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------PEPT_TRNA_H------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td2 A   1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPAQNR 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain A from PDB  Type:PROTEIN  Length:187
 aligned with PTH_MYCTU | P9WHN7 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
            PTH_MYCTU     1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPAQNR 187
               SCOP domains d3td2a_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhhhh....ee......eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhhh....eeeeee........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------PEPT_TRNA_HYDR------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------PEPT_TRNA_H------------------------------------------------------------------ PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td2 A   1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPAQNR 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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)

d3td2a_

(no "CATH Domain" information available for 3TD2)

(no "Pfam Domain" information available for 3TD2)

Asymmetric/Biological Unit(hide GO term definitions)

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.

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3td2)

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	3td2
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	PTH_MYCTO \| P9WHN6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	PTH_MYCTU \| P9WHN7
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.1.1.29
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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Access by UniProt ID/Accession number
	PTH_MYCTO \| P9WHN6
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	PTH_MYCTU \| P9WHN7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PTH_MYCTO \| P9WHN6	:	2jrc 2z2i 2z2j 2z2k 3tck 3tcn 3td6
	PTH_MYCTU \| P9WHN7	:	2jrc 2z2i 2z2j 2z2k 3tck 3tcn 3td6

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 10)

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