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(-) Description

Title :  PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM TUBERCULOSIS FROM TRIGONAL PARTIALLY DEHYDRATED CRYSTAL
 
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 :  3.20
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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3TD6)

(-) Sites  (0, 0)

(no "Site" information available for 3TD6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TD6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TD6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TD6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPT_TRNA_HYDROL_1PS01195 Peptidyl-tRNA hydrolase signature 1.PTH_MYCTO17-30  1A:17-30
PTH_MYCTU17-30  1A:17-30
2PEPT_TRNA_HYDROL_2PS01196 Peptidyl-tRNA hydrolase signature 2.PTH_MYCTO111-121  1A:111-121
PTH_MYCTU111-121  1A:111-121

(-) Exons   (0, 0)

(no "Exon" information available for 3TD6)

(-) Sequences/Alignments

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:184
 aligned with PTH_MYCTO | P9WHN6 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
            PTH_MYCTO     1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPA 184
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhhhhh....ee......eeeeeee..eeeeeee.......hhhhhhhhhh....hhh.eeeeeee.......eeeee........hhhhhhhhhh....eeeeee........hhhhhh......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PEPT_TRNA_HYDR---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------PEPT_TRNA_H--------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td6 A   1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPA 184
                                    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:184
 aligned with PTH_MYCTU | P9WHN7 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
            PTH_MYCTU     1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPA 184
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhhhhh....ee......eeeeeee..eeeeeee.......hhhhhhhhhh....hhh.eeeeeee.......eeeee........hhhhhhhhhh....eeeeee........hhhhhh......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------PEPT_TRNA_HYDR---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------PEPT_TRNA_H--------------------------------------------------------------- PROSITE (1)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td6 A   1 MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPA 184
                                    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)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3TD6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TD6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TD6)

(-) Gene Ontology  (6, 10)

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.

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  3.1.1.29
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PTH_MYCTO | P9WHN6: 2jrc 2z2i 2z2j 2z2k 3tck 3tcn 3td2
        PTH_MYCTU | P9WHN7: 2jrc 2z2i 2z2j 2z2k 3tck 3tcn 3td2

(-) Related Entries Specified in the PDB File

2jrc 2pth 2z2i 2z2j 2z2k 3p2j 3tck 3tcn 3td2