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(-) Description

Title :  PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE Y84F MUTANT WITH DUPNHPP).
 
Authors :  M. A. Tormo-Mas, J. Donderis, M. Garcia-Caballer, A. Alt, I. Mir-Sanch A. Marina, J. R. Penades
Date :  10 Dec 12  (Deposition) - 30 Jan 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Hydrolase, Pathogenicity Island, Sapi Induction, Gene Transfer, Moonlighting Proteins, G-Protein, P-Loop (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Tormo-Mas, J. Donderis, M. Garcia-Caballer, A. Alt, I. Mir-Sanchis, A. Marina, J. R. Penades
Phage Dutpases Control Transfer Of Virulence Genes By A Proto-Oncogenic G Protein-Like Mechanism.
Mol. Cell V. 49 947 2013
PubMed-ID: 23333307  |  Reference-DOI: 10.1016/J.MOLCEL.2012.12.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DUTPASE
    Chains: A
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS PHAGE 80ALPHA
    Organism Taxid: 53369
    Other Details: STRUCTURE IN PRESENCE OF DUMP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:20 , ARG A:64 , SER A:65 , GLY A:66 , GLY A:78 , LYS A:79 , ILE A:80 , ASP A:81 , PHE A:84 , LEU A:88 , GLY A:89 , GLN A:137 , ARG A:160 , GLY A:164 , PHE A:165 , GLY A:166 , SER A:167 , SER A:168 , MG A:1173 , HOH A:2009 , HOH A:2017 , HOH A:2033BINDING SITE FOR RESIDUE DUP A 777
2AC2SOFTWAREASP A:28 , ARG A:64 , DUP A:777 , HOH A:2033BINDING SITE FOR RESIDUE MG A1173
3AC3SOFTWAREHIS A:72 , HIS A:96 , ARG A:107BINDING SITE FOR RESIDUE NI A1171
4AC4SOFTWAREASP A:95 , HOH A:2018BINDING SITE FOR RESIDUE NI A1172

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZF5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZF5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZF5)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZF5)

(-) 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:169
 aligned with A4ZF98_9CAUD | A4ZF98 from UniProtKB/TrEMBL  Length:170

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
         A4ZF98_9CAUD     2 TNTLQVKLLSKNARMPERNHKTDAGYDIFSAETVVLEPQEKAVIKTDVAVSIPEGYVGLLTSRSGVSSKTHLVIETGKIDAGYHGNLGINIKNDHEDDKMQTIFLRNIDNEKIFEKERHLYKLGSYRIEKGERIAQLVIVPIWTPELKQVEEFESVSERGEKGFGSSGV 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.................eeee....eee....eeeee..eeee....eeeeeeehhhhhhhh.eee..eee........eeeeee.......ee..................ee...eee....eeeeeeeee............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zf5 A   2 TNTLQVKLLSKNARMPERNHKTDAGYDIFSAETVVLEPQEKAVIKTDVAVSIPEGYVGLLTSRSGVSSKTHLVIETGKIDAGFHGNLGINIKNDHEDDKMQTIFLRNIDNEKIFEKERHLYKLGSYRIEKGERIAQLVIVPIWTPELKQVEEFESVSERGEKGFGSSGV 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3ZF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZF5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (A4ZF98_9CAUD | A4ZF98)
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.
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
        A4ZF98_9CAUD | A4ZF98: 3zez 3zf0 3zf1 3zf2 3zf3 3zf4 3zf6 5cco 5cct

(-) Related Entries Specified in the PDB File

3zez PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE WITH DUPNHPP).
3zf0 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE D81A MUTANT WITH DUPNHPP).
3zf1 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE D81N MUTANT WITH DUPNHPP).
3zf2 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE).
3zf3 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE Y84I MUTANT).
3zf4 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE Y81A MUTANT WITH DUPNHPP).
3zf6 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE D81A D110C S168C MUTANT WITH DUPNHPP).