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(-) Description

Title :  CRYSTAL STRUCTURE OF PROJECT ID PH1539 FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  K. Shimizu, N. Kunishima, Riken Structural Genomics/Proteomics I (Rsgi)
Date :  26 Jul 04  (Deposition) - 19 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (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

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A
    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: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: CGI-147 PROTEIN, PTH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:89 , HOH A:1020 , HOH A:1045 , HOH A:1047 , HOH A:1056 , HOH A:1174BINDING SITE FOR RESIDUE NA A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WN2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:104 -Pro A:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WN2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WN2)

(-) Exons   (0, 0)

(no "Exon" information available for 1WN2)

(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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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 d1wn2a_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --PTH2-1wn2A01 A:6-121                                                                                                 Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eeeee...........eeeeeeeeeehhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1wn2 A   4 MFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAWFREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTVLAVGPAPEEIVDKVTGNLKLL 121
                                    13        23        33        43        53        63        73        83        93       103       113
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WN2)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PTH2 (5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (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: 2d3k

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