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(-) Description

Title :  EBV DUTPASE MUTANT CYS4SER
 
Authors :  L. Freeman, M. Buisson, N. Tarbouriech, W. P. Burmeister
Date :  27 Mar 09  (Deposition) - 07 Jul 09  (Release) - 15 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Dutpase, Monomer, Hydrolase, Human Herpes Virus, Epstein- Barr Virus, Nucleotide Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Freeman, M. Buisson, N. Tarbouriech, A. Van Der Heyden, P. Labbe, W. P. Burmeister
The Flexible Motif V Of Epstein-Barr Virus Deoxyuridine 5'-Triphosphate Pyrophosphatase Is Essential For Catalysis.
J. Biol. Chem. V. 284 25280 2009
PubMed-ID: 19586911  |  Reference-DOI: 10.1074/JBC.M109.019315
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTB
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Common: EPSTEIN-BARR VIRUS
    Organism Scientific: HUMAN HERPESVIRUS 4
    Organism Taxid: 10377
    Strain: B95-8
    Synonym: DUTP PYROPHOSPHATASE, DUTPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2TEO1Ligand/IonMALATE LIKE INTERMEDIATE
3UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:71 , GLY A:73 , ASP A:76 , LEU A:83 , ARG A:84 , ASN A:94 , ARG A:171 , SER A:172 , HOH A:2066 , HOH A:2169 , HOH A:2170 , HOH A:2171 , HOH A:2172 , HOH A:2173BINDING SITE FOR RESIDUE UMP A1257
2AC2SOFTWAREHIS A:163 , ARG A:165 , LYS A:219BINDING SITE FOR RESIDUE SO4 A1258
3AC3SOFTWARELEU A:35 , ARG A:37 , ASP A:76 , GLY A:78 , TYR A:79 , ASN A:94 , ASP A:131 , HOH A:2173BINDING SITE FOR RESIDUE TEO A1259

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WE0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:121 -Pro A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WE0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WE0)

(-) Exons   (0, 0)

(no "Exon" information available for 2WE0)

(-) 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:247
 aligned with DUT_EBVB9 | P03195 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:252
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
            DUT_EBVB9     5 PHIRYAFQNDKLLLQQASVGRLTLVNKTTILLRPMKTTTVDLGLYARPPEGHGLMLWGSTSRPVTSHVGIIDPGYTGELRLILQNQRRYNSTLRPSELKIHLAAFRYATPQMEEDKGPINHPQYPGDVGLDVSLPKDLALFPHQTVSVTLTVPPPSIPHHRPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVYLHKHHLTSFYSPHSDAGVLGPRSLFRWASCTFEEVPSLAM 256
               SCOP domains d2we0a1 A:5-115 automated matches                                                                              -----d2we0a2 A:121-256 automated matches                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------dUTPase-2we0A01 A:121-240                                                                                               ---------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeee..eeeeee...eee....eeeeeeeeeee....eeeeeeee....eee..eee.......eeeeeee.....eee.....eeeeeeeeee...-----.....................eee...eeeeeee................hhhhhhh.eee.........eeeeeee.....eee....eeeeeeeee...ee......ee........eee....eeee.hhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2we0 A   5 PHIRYAFQNDKLLLQQASVGRLTLVNKTTILLRPMKTTTVDLGLYARPPEGHGLMLWGSTSRPVTSHVGIIDPGYTGELRLILQNQRRYNSTLRPSELKIHLAAFRYATPQ-----GPINHPQYPGDVGLDVSLPKDLALFPHQTVSVTLTVPPPSIPHHRPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVYLHKHHLTSFYSPHSDAGVLGPRSLFRWASCTFEEVPSLAM 256
                                    14        24        34        44        54        64        74        84        94       104       114|     |124       134       144       154       164       174       184       194       204       214       224       234       244       254  
                                                                                                                                        115   121
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WE0)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DUT_EBVB9 | P03195)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_EBVB9 | P03195: 2bsy 2bt1 2we1 2we2 2we3

(-) Related Entries Specified in the PDB File

2bsy EPSTEIN BARR VIRUS DUTPASE
2bt1 EPSTEIN BARR VIRUS DUTPASE IN COMPLEX WITH A,B-IMINO DUTP
2we1 EBV DUTPASE MUTANT ASP131ASN WITH BOUND DUMP
2we2 EBV DUTPASE DOUBLE MUTANT GLY78ASP-ASP131SER WITH DUMP
2we3 EBV DUTPASE INACTIVE MUTANT DELETED OF MOTIF V