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(-) Description

Title :  EBV DUTPASE MUTANT ASP131ASN WITH BOUND DUMP
 
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 :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Pyrophosphatase, Epstein-Barr Virus, Nucleotide Metabolism, Dutpase, Monomer, Hydrolase, Herpes Virus (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: DUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:60 , HIS A:71 , GLY A:73 , ILE A:74 , ILE A:75 , ASP A:76 , TYR A:79 , LEU A:83 , ARG A:84 , ASN A:94 , ARG A:171 , SER A:172 , HOH A:2069 , HOH A:2071 , HOH A:2088 , HOH A:2216 , HOH A:2217 , HOH A:2218 , HOH A:2219 , HOH A:2220BINDING SITE FOR RESIDUE UMP A1257
2AC2SOFTWARECYS A:184 , ARG A:185 , ARG A:187 , ARG A:238 , SER A:239 , HOH A:2221BINDING SITE FOR RESIDUE SO4 A1258
3AC3SOFTWAREHIS A:163 , ARG A:165 , LYS A:219 , HOH A:2222BINDING SITE FOR RESIDUE SO4 A1259
4AC4SOFTWAREGLN A:19 , LYS A:103 , HIS A:105 , LYS A:140 , HOH A:2223 , HOH A:2224 , HOH A:2225BINDING SITE FOR RESIDUE SO4 A1260

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:246

(-) 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 2WE1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WE1)

(-) Exons   (0, 0)

(no "Exon" information available for 2WE1)

(-) 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:245
 aligned with DUT_EBVB9 | P03195 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
            DUT_EBVB9     4 CPHIRYAFQNDKLLLQQASVGRLTLVNKTTILLRPMKTTTVDLGLYARPPEGHGLMLWGSTSRPVTSHVGIIDPGYTGELRLILQNQRRYNSTLRPSELKIHLAAFRYATPQMEEDKGPINHPQYPGDVGLDVSLPKDLALFPHQTVSVTLTVPPPSIPHHRPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVYLHKHHLTSFYSPHSDAGVLGPRSLFRWASCTFEEVPSLAM 256
               SCOP domains d2we1a1 A:4-116 automated matches                                                                                    d2we    1a2 A:121-256 automated matches                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeeee..eeeeee...eee....eeeeeeeeeee....eeeeeeee....eee..eee.......eeeeeee.....eee.....eeeeeeeeee....----....----.............eee...eeeeeee................hhhhhhh.eee.........eeeeeee.....eee....eeeeeeeee...ee......ee........eee.....eee.hhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2we1 A   4 CPHIRYAFQNDKLLLQQASVGRLTLVNKTTILLRPMKTTTVDLGLYARPPEGHGLMLWGSTSRPVTSHVGIIDPGYTGELRLILQNQRRYNSTLRPSELKIHLAAFRYATPQM----GPIN----PGNVGLDVSLPKDLALFPHQTVSVTLTVPPPSIPHHRPTIFGRSGLAMQGILVKPCRWRRGGVDVSLTNFSDQTVFLNKYRRFCQLVYLHKHHLTSFYSPHSDAGVLGPRSLFRWASCTFEEVPSLAM 256
                                    13        23        33        43        53        63        73        83        93       103       113  |    123|    | 133       143       153       163       173       183       193       203       213       223       233       243       253   
                                                                                                                                          116  121  |  129                                                                                                                               
                                                                                                                                                  124
   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 2WE1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WE1)

(-) 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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  2we1
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  DUT_EBVB9 | P03195
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  3.6.1.23
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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_EBVB9 | P03195: 2bsy 2bt1 2we0 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
2we0 EBV DUTPASE MUTANT CYS4SER
2we2 EBV DUTPASE DOUBLE MUTANT GLY78ASP-ASP131SER WITH DUMP
2we3 EBV DUTPASE INACTIVE MUTANT DELETED OF MOTIF V