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(-) Description

Title :  STRUCTURE OF THE E. COLI INOSINE TRIPHOSPHATE PYROPHOSPHATASE RGDB IN COMPLEX WITH IMP
 
Authors :  A. U. Singer, M. Proudfoot, T. Skarina, A. Savchenko, A. F. Yakunin
Date :  16 May 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Itp Pyrophosphatase X-Ray Structure Enzyme Mechanism Product, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Savchenko, M. Proudfoot, T. Skarina, A. Singer, O. Litvinova, R. Sanishvili, G. Brown, N. Chirgadze, A. F. Yakunin
Molecular Basis Of The Antimutagenic Activity Of The House-Cleaning Inosine Triphosphate Pyrophosphatase Rdgb From Escherichia Coli.
J. Mol. Biol. V. 374 1091 2007
PubMed-ID: 17976651  |  Reference-DOI: 10.1016/J.JMB.2007.10.012

(-) Compounds

Molecule 1 - INOSINE TRIPHOSPHATE PYROPHOSPHATASE RDGB
    Chains: A
    EC Number: 3.6.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15-B-BASED,P11
    Expression System Strain: BL21(DE3) CODON PLUS RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YGGV
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 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
1EDO1Ligand/Ion1,2-ETHANEDIOL
2IMP1Ligand/IonINOSINIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2IMP2Ligand/IonINOSINIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , GLY A:71 , SER A:85 , ALA A:86 , PHE A:118 , PHE A:154 , TYR A:156 , ASP A:157 , LYS A:177 , HIS A:182 , HOH A:3067 , HOH A:3074 , HOH A:3106BINDING SITE FOR RESIDUE IMP A 3036
2AC2SOFTWAREPRO A:81 , GLY A:82 , ILE A:83 , HOH A:3040BINDING SITE FOR RESIDUE EDO A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:-3 -Gly A:-2
2Ala A:80 -Pro A:81
3Arg A:195 -Asn A:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PYU)

(-) 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:208
 aligned with IXTPA_ECOLI | P52061 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:208
                                        1                                                                                                                                                                                                   
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188        
          IXTPA_ECOLI     - ------------MQKVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADDSGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETMKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALRN 196
               SCOP domains d2pyua_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2pyuA00 A:-11-196  [code=3.90.950.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee...hhhhhhhhhhhhh...eeeee..............hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhhhhh.....hhhhhhhhhhhhhh..hhhh.eeeeeeeeeee........eeeeeeeeeee...........hhh.eehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyu A -11 HHSSGLVPRGSHMQKVVLATGNVGKVRELASLLSDFGLDIVAQTDLGVDSAEETGLTFIENAILKARHAAKVTALPAIADASGLAVDVLGGAPGIYSARYSGEDATDQKNLQKLLETMKDVPDDQRQARFHCVLVYLRHAEDPTPLVCHGSWPGVITREPAGTGGFGYDPIFFVPSEGKTAAELTREEKSAISHRGQALKLLLDALRN 196
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   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, 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 2PYU)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (IXTPA_ECOLI | P52061)
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: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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IXTPA_ECOLI | P52061: 1k7k 2q16

(-) Related Entries Specified in the PDB File

1k7k STRUCTURE OF APO-RGDB
2q16 YGGV PLUS ITP