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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN OF UNKNOWN FUNCTION FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  J. Jeyakanthan, T. H. Tahirov, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  21 Jan 04  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Trna Synthetase, Nucleotide Binding Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, E. Inagaki, C. Kuroishi, T. H. Tahirov
Structure Of Pin-Domain Protein Ph0500 From Pyrococcus Horikoshii.
Acta Crystallogr. , Sect. F V. 61 463 2005
PubMed-ID: 16511069  |  Reference-DOI: 10.1107/S1744309105012406

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH0500
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21-CODON PLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1054 , SER B:110 , GLY B:127 , ASP B:129 , HOH B:1119BINDING SITE FOR RESIDUE GOL B 1001
2AC2SOFTWAREALA A:105 , ASN A:109 , SER A:110 , GLY A:127 , LEU A:128 , ASP A:129 , HOH A:1089 , HOH A:1175 , HOH A:1242BINDING SITE FOR RESIDUE GOL A 1002
3AC3SOFTWARELYS A:138 , GLU A:141 , HOH A:1010 , HOH A:1011 , HOH A:1017 , ARG B:49BINDING SITE FOR RESIDUE GOL A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V96)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V96)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V96)

(-) Exons   (0, 0)

(no "Exon" information available for 1V96)

(-) 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:146
 aligned with VAPC4_PYRHO | O58236 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          VAPC4_PYRHO     2 PLPPDITFDSLALIKMHSQNMKRILEVTLAKFTVNLSIVTVYRYLTARAYLKKNIEAEFEILKDIYNIVPLLDDIAIKAAQIEANLIKKEITLDMEDIITATTAIYTNSLLVTDDPKRYEPIRRFGLDTMPLDKFIKEVELMVEKELI 149
               SCOP domains d1v96a1 A:2-149 Hypothetical protein PH0500                                                                                                          SCOP domains
               CATH domains 1v96A00 A:2-149 5'-nuclease                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhh--...hhhhhhhhhhhhheee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh..eeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v96 A   2 PLPPDITFDSLALIKMHSQNMKRILEVTLAKFTVNLSIVTVYRYLTAR--LKKNIEAEFEILKDIYNIVPLLDDIAIKAAQIEANLIKKEITLDMEDIITATTAIYTNSLLVTDDPKRYEPIRRFGLDTMPLDKFIKEVELMVEKELI 149
                                    11        21        31        41       | -|       61        71        81        91       101       111       121       131       141        
                                                                          49 52                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with VAPC4_PYRHO | O58236 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    
          VAPC4_PYRHO     2 PLPPDITFDSLALIKMHSQNMKRILEVTLAKFTVNLSIVTVYRYLTARAYLKKNIEAEFEILKDIYNIVPLLDDIAIKAAQIEANLIKKEITLDMEDIITATTAIYTNSLLVTDDPKRYEPIRRFGLDTMPLDKFIKEVELMVE 145
               SCOP domains d1v96b_ B: Hypothetical protein PH0500                                                                                                           SCOP domains
               CATH domains 1v96B00 B:2-145 5'-nuclease                                                                                                                      CATH domains
           Pfam domains (1) -----PIN-1v96B01 B:7-125                                                                                                    -------------------- Pfam domains (1)
           Pfam domains (2) -----PIN-1v96B02 B:7-125                                                                                                    -------------------- Pfam domains (2)
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhheee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v96 B   2 PLPPDITFDSLALIKMHSQNMKRILEVTLAKFTVNLSIVTVYRYLTARAYLKKNIEAEFEILKDIYNIVPLLDDIAIKAAQIEANLIKKEITLDMEDIITATTAIYTNSLLVTDDPKRYEPIRRFGLDTMPLDKFIKEVELMVE 145
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PIN (27)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VAPC4_PYRHO | O58236)
molecular function
    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.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VAPC4_PYRHO | O58236: 1ye5 5h4g 5h4h

(-) Related Entries Specified in the PDB File

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