Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) 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
    ChainsA
    EC Number3.1.1.29
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSETBMTUPTH
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMT1042, MTCY10G2.35, PTH, RV1014C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    StrainH37RV
    SynonymPTH

 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)
    → 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 '|'

 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3td6)
 
  Sites
(no "Sites" information available for 3td6)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3td6)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3td6
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PTH_MYCTO | P9WHN6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  PTH_MYCTU | P9WHN7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.1.29
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PTH_MYCTO | P9WHN6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PTH_MYCTU | P9WHN7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PTH_MYCTO | P9WHN62jrc 2z2i 2z2j 2z2k 3tck 3tcn 3td2
        PTH_MYCTU | P9WHN72jrc 2z2i 2z2j 2z2k 3tck 3tcn 3td2

(-) Related Entries Specified in the PDB File

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