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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
 
Authors :  N. Schormann, D. Chattopadhyay
Date :  16 Jan 07  (Deposition) - 01 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Fold, Jelly-Roll, Superfamily, Dutpase-Like, Forms Tight Trimer Through An Additional Beta-Sheet In Each Subunit, Subunit Beta- Sheets Are Orthogonally Packed Around The Three-Fold Axis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Samal, N. Schormann, W. J. Cook, L. J. Delucas, D. Chattopadhyay
Structures Of Vaccinia Virus Dutpase And Its Nucleotide Complexes.
Acta Crystallogr. , Sect. D V. 63 571 2007
PubMed-ID: 17452782  |  Reference-DOI: 10.1107/S0907444907007871

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    ChainsA, B, C
    EC Number3.6.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDUT
    Organism ScientificVACCINIA VIRUS
    Organism Taxid10245
    SynonymDUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:63 , ARG A:65 , GLN A:118 , ARG B:65 , GLN B:118 , GLN C:118BINDING SITE FOR RESIDUE CL A 200
2AC2SOFTWAREASP A:78 , HOH A:212 , ILE B:79 , ILE B:97BINDING SITE FOR RESIDUE EDO A 201
3AC3SOFTWAREGLY A:82 , GLY A:93 , ILE A:95 , HOH A:210 , SER C:70BINDING SITE FOR RESIDUE EDO A 202
4AC4SOFTWARESER A:70 , GLY B:82 , GLY B:93 , ILE B:95 , HOH B:218BINDING SITE FOR RESIDUE EDO B 203
5AC5SOFTWARETYR A:63 , GLN A:118 , ARG A:119 , ILE A:120 , GLN B:118 , ARG B:119 , GLN C:118 , ARG C:119BINDING SITE FOR RESIDUE EDO A 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OKD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OKD)

(-) 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:124
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:124
                                    18        28        38        48        58        68        78        88        98       108       118       128    
         A4GD96_9POXV     9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSLD 132
               SCOP domains d2okda_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                        SCOP domains
               CATH domains 2okdA00 A:9-132  [code=2.70.40.10, no name defined]                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.................eeee....eee...eeeeee..eee.....eeeeee.hhhhhh..eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okd A   9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSLD 132
                                    18        28        38        48        58        68        78        88        98       108       118       128    

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:123
                                    18        28        38        48        58        68        78        88        98       108       118       128   
         A4GD96_9POXV     9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
               SCOP domains d2okdb_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                       SCOP domains
               CATH domains 2okdB00 B:9-131  [code=2.70.40.10, no name defined]                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.................eeee....eee...eeeeee..eee.....eeeeee.hhhhhh..eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okd B   9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    18        28        38        48        58        68        78        88        98       108       118       128   

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:125
                                    16        26        36        46        56        66        76        86        96       106       116       126     
         A4GD96_9POXV     7 NSPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
               SCOP domains d2okdc_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                         SCOP domains
               CATH domains 2okdC00 C:7-131  [code=2.70.40.10, no name defined]                                                                           CATH domains
           Pfam domains (1) ----------dUTPase-2okdC01 C:17-131                                                                                            Pfam domains (1)
           Pfam domains (2) ----------dUTPase-2okdC02 C:17-131                                                                                            Pfam domains (2)
           Pfam domains (3) ----------dUTPase-2okdC03 C:17-131                                                                                            Pfam domains (3)
         Sec.struct. author ...eeeee.................eeee....eee....eeeee..eee.....eeeeee.hhhhhhh.eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okd C   7 NSPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    16        26        36        46        56        66        76        86        96       106       116       126     

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (A4GD96_9POXV | A4GD96)
molecular function
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    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:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.

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 Related Entries

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

UniProtKB/TrEMBL
        A4GD96_9POXV | A4GD962okb 2oke 2ol0 2ol1

(-) Related Entries Specified in the PDB File

1q5u HUMAN DUTPASE
2okb N-TERMINALLY TRUNCATED VERSION OF VACCINIA VIRUS DUTPASE
2oke HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
2ol0 HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
2ol1 HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE