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(-) Description

Title :  STRUCTURE OF NUCLEOTIDE TRIPHOSPHATE PYROPHOSPHATASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  H. Mizutani, N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Dec 06  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  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 :  H. Mizutani, N. K. Lokanath, N. Kunishima
Structure Of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH1917
    Chains: A
    EC Number: 3.6.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ITT1Ligand/IonINOSINE 5'-TRIPHOSPHATE
3NA3Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2ITT2Ligand/IonINOSINE 5'-TRIPHOSPHATE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:34 , GLU A:36 , GLU A:64 , ASP A:65 , ITT A:201 , NA A:302 , HOH A:595BINDING SITE FOR RESIDUE NA A 301
2AC2SOFTWAREGLU A:36 , ITT A:201 , NA A:301 , NA A:303 , HOH A:450 , HOH A:580BINDING SITE FOR RESIDUE NA A 302
3AC3SOFTWAREGLU A:36 , ASP A:65 , ITT A:201 , NA A:302 , HOH A:413 , HOH A:445 , HOH A:579BINDING SITE FOR RESIDUE NA A 303
4AC4SOFTWARETHR A:7 , SER A:8 , ASN A:9 , LYS A:12 , GLU A:36 , GLU A:64 , ASP A:65 , SER A:66 , SER A:81 , SER A:82 , TYR A:85 , PHE A:107 , PHE A:140 , GLY A:141 , TYR A:142 , ASP A:143 , LYS A:163 , HIS A:168 , ARG A:169 , NA A:301 , NA A:302 , NA A:303 , HOH A:414 , HOH A:440 , HOH A:450 , HOH A:551 , HOH A:580BINDING SITE FOR RESIDUE ITT A 201
5AC5SOFTWAREGLU A:43 , LYS A:121 , SER A:123BINDING SITE FOR RESIDUE EDO A 401
6AC6SOFTWAREPRO A:58 , PHE A:69 , ILE A:70 , GLU A:71 , GLY A:75 , TYR A:106 , HOH A:550BINDING SITE FOR RESIDUE EDO A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E5X)

(-) 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 2E5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E5X)

(-) Exons   (0, 0)

(no "Exon" information available for 2E5X)

(-) 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 d2e5xa_ A: XTP pyrophosphatase                                                                                                                                                            SCOP domains
               CATH domains 2e5xA00 A:1-185  [code=3.90.950.10, no name defined]                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhh......eeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee..eeeeeeeeeeeee...........hhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e5x A   1 MKIFFITSNPGKVREVANFLGTFGIEIVQLKHEYPEIQAEKLEDVVDFGISWLKGKVPEPFMIEDSGLFIESLKGFPGVYSSYVYRTIGLEGILKLMEGAEDRRAYFKSVIGFYIDGKAYKFSGVTWGRISNEKRGTHGFGYDPIFIPEGSQKTFAEMTIEEKNALSHRGKALKAFFEWLKVNLK 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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  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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E5X)

(-) 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

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

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