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(-) Description

Title :  STRUCTURE OF PH1917 PROTEIN WITH THE COMPLEX OF ITP FROM PYROCOCCUS HORIKOSHII
 
Authors :  N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  31 Jul 06  (Deposition) - 04 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ntpase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, K. J. Pampa, K. Takio, N. Kunishima
Structures Of Dimeric Nonstandard Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii Ot3: Functional Significance Of Interprotomer Conformational Changes
J. Mol. Biol. V. 375 1013 2008
PubMed-ID: 18062990  |  Reference-DOI: 10.1016/J.JMB.2007.11.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH1917
    Chains: A
    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
    Synonym: NTPASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ITT1Ligand/IonINOSINE 5'-TRIPHOSPHATE
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ITT2Ligand/IonINOSINE 5'-TRIPHOSPHATE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:12 , TYR A:34 , GLU A:36 , GLU A:64 , ASP A:65 , ITT A:201BINDING SITE FOR RESIDUE NA A 301
2AC2SOFTWARETHR A:7 , SER A:8 , ASN A:9 , LYS A:12 , GLU A:36 , GLU A:64 , ASP A:65 , SER A:66 , GLY A:67 , SER A:81 , SER A:82 , PHE A:107 , PHE A:140 , TYR A:142 , ASP A:143 , LYS A:163 , HIS A:168 , ARG A:169 , NA A:301 , HOH A:318 , HOH A:325 , HOH A:341BINDING SITE FOR RESIDUE ITT A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:59 -Pro A:60
2Phe A:76 -Pro A:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DVO)

(-) Sequences/Alignments

Asymmetric 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:185
 aligned with IXTPA_PYRHO | O59580 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
          IXTPA_PYRHO     1 MKIFFITSNPGKVREVANFLGTFGIEIVQLKHEYPEIQAEKLEDVVDFGISWLKGKVPEPFMIEDSGLFIESLKGFPGVYSSYVYRTIGLEGILKLMEGAEDRRAYFKSVIGFYIDGKAYKFSGVTWGRISNEKRGTHGFGYDPIFIPEGSEKTFAEMTIEEKNALSHRGKALKAFFEWLKVNLK 185
               SCOP domains d2dvoa_ A: XTP pyrophosphatase                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhh......eeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeee...........hhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvo A   1 MKIFFITSNPGKVREVANFLGTFGIEIVQLKHEYPEIQAEKLEDVVDFGISWLKGKVPEPFMIEDSGLFIESLKGFPGVYSSYVYRTIGLEGILKLMEGAEDRRAYFKSVIGFYIDGKAYKFSGVTWGRISNEKRGTHGFGYDPIFIPEGSEKTFAEMTIEEKNALSHRGKALKAFFEWLKVNLK 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
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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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (IXTPA_PYRHO | O59580)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0047429    nucleoside-triphosphate diphosphatase activity    Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009143    nucleoside triphosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IXTPA_PYRHO | O59580: 1v7r 2dvn 2dvp 2e5x 2zti

(-) Related Entries Specified in the PDB File

2dvn THE SAME PROTEIN WITH THE COMPLEX OF IMP
2dvp THE SAME PROTEIN WITHOUT LIGANDS RELATED ID: PHO001001917.3 RELATED DB: TARGETDB