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(-) Description

Title :  STRUCTURAL STUDY ON PROJECT ID PH1539 FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  K. Shimizu, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Sep 05  (Deposition) - 29 Mar 06  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shimizu, C. Kuroishi, M. Sugahara, N. Kunishima
Structure Of Peptidyl-Trna Hydrolase 2 From Pyrococcus Horikoshii Ot3: Insight Into The Functional Role Of Its Dimeric State.
Acta Crystallogr. , Sect. D V. 64 444 2008
PubMed-ID: 18391411  |  Reference-DOI: 10.1107/S0907444908002850
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A, B
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLAMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: PTH, CGI-147 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:108 , ASP A:112 , GLU B:108 , ASP B:112BINDING SITE FOR RESIDUE ZN B 1001
2AC2SOFTWAREGLU B:66 , GLU B:76BINDING SITE FOR RESIDUE ZN B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D3K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:104 -Pro A:105
2Gly B:104 -Pro B:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D3K)

(-) Exons   (0, 0)

(no "Exon" information available for 2D3K)

(-) 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:118
 aligned with PTH_PYRHO | O74017 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    13        23        33        43        53        63        73        83        93       103       113        
            PTH_PYRHO     4 MFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAWFREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTVLAVGPAPEEIVDKVTGNLKLL 121
               SCOP domains d2d3ka_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh..eeeee...........eeeeeeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3k A   4 MFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAWFREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTVLAVGPAPEEIVDKVTGNLKLL 121
                                    13        23        33        43        53        63        73        83        93       103       113        


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PTH_PYRHO | O74017 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    13        23        33        43        53        63        73        83        93       103       113        
            PTH_PYRHO     4 MFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAWFREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTVLAVGPAPEEIVDKVTGNLKLL 121
               SCOP domains d2d3kb_ B: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee...........eeeeeeeeeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3k B   4 MFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAWFREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTVLAVGPAPEEIVDKVTGNLKLL 121
                                    13        23        33        43        53        63        73        83        93       103       113
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D3K)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PTH_PYRHO | O74017)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        PTH_PYRHO | O74017: 1wn2

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