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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
 
Authors :  N. Schormann, D. Chattopadhyay
Date :  18 Jan 07  (Deposition) - 01 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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
    Chains: A, B, C
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DUT
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 10245
    Synonym: DUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3UMP3Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:65 , GLN A:118 , TYR B:63 , ARG B:65 , GLN B:118 , GLN C:118BINDING SITE FOR RESIDUE CL A 301
2AC2SOFTWAREGLY A:82 , VAL A:83 , ILE A:84 , ASP A:85 , TYR A:88 , GLY A:93 , HOH A:304 , ARG C:69 , SER C:70 , GLY C:71 , HOH C:1222 , HOH C:1267 , HOH C:1289 , HOH C:1292BINDING SITE FOR RESIDUE UMP C 1201
3AC3SOFTWARESER A:70 , GLY B:82 , VAL B:83 , ILE B:84 , ASP B:85 , TYR B:88 , GLY B:93 , HOH B:225 , HOH C:1207 , HOH C:1291 , HOH C:1301BINDING SITE FOR RESIDUE UMP C 1202
4AC4SOFTWAREARG B:69 , SER B:70 , GLY C:82 , VAL C:83 , ILE C:84 , ASP C:85 , TYR C:88 , GLY C:93 , HOH C:1204 , HOH C:1290 , HOH C:1293BINDING SITE FOR RESIDUE UMP C 1203
5AC5SOFTWAREARG B:119 , PHE C:61 , CYS C:62 , ARG C:119 , ILE C:120BINDING SITE FOR RESIDUE EDO C 401
6AC6SOFTWAREGLN A:118 , ARG A:119 , GLN B:118 , ARG B:119 , GLN C:118 , ARG C:119BINDING SITE FOR RESIDUE EDO C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OL1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OL1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OL1)

(-) Exons   (0, 0)

(no "Exon" information available for 2OL1)

(-) 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
                                    17        27        37        47        57        67        77        87        97       107       117       127    
         A4GD96_9POXV     8 SPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
               SCOP domains d2ol1a_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                        SCOP domains
               CATH domains 2ol1A00 A:8-131  [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
                 2ol1 A   8 SPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    17        27        37        47        57        67        77        87        97       107       117       127    


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:124
                                    17        27        37        47        57        67        77        87        97       107       117       127    
         A4GD96_9POXV     8 SPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
               SCOP domains d2ol1b_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                        SCOP domains
               CATH domains 2ol1B00 B:8-131  [code=2.70.40.10, no name defined]                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.................eeee....eee...eeeeee..eee.....eeeeee.hhhhhhh.eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ol1 B   8 SPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    17        27        37        47        57        67        77        87        97       107       117       127    


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 d2ol1c_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                         SCOP domains
               CATH domains 2ol1C00 C:7-131  [code=2.70.40.10, no name defined]                                                                           CATH domains
           Pfam domains (1) ----------dUTPase-2ol1C01 C:17-131                                                                                            Pfam domains (1)
           Pfam domains (2) ----------dUTPase-2ol1C02 C:17-131                                                                                            Pfam domains (2)
           Pfam domains (3) ----------dUTPase-2ol1C03 C:17-131                                                                                            Pfam domains (3)
         Sec.struct. author ...eeeee.................eeee....eee...eeeeee..eee.....eeeeee.hhhhhhh.eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ol1 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
(-)
Class: All beta proteins (24004)

(-) 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 | A4GD96: 2okb 2okd 2oke 2ol0

(-) Related Entries Specified in the PDB File

2okb N-TERMINALLY TRUNCATED VERSION OF VACCINIA VIRUS DUTPASE
2okd APO-ENZYME OF VACCINIA VIRUS DUTPASE
2oke STRUCTURE OF VACCINIA VIRUS DUTPASE WITH SUBSTRATE ANALOG
2ol0 STRUCTURE OF VACCINIA VIRUS DUTPASE WITH INHIBITOR