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(-) Description

Title :  CRYSTAL STRUCTURE OF M-PMV DUTPASE WITH A MIXED POPULATION OF SUBSTRATE (DUPNPP) AND POST-INVERSION PRODUCT (DUMP) IN THE ACTIVE SITES
 
Authors :  O. Barabas, V. Nemeth, B. G. Vertessy
Date :  09 Sep 11  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Jelly Roll, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Barabas, V. Nemeth, A. Bodor, A. Perczel, E. Rosta, Z. Kele, I. Zagyva, Z. Szabadka, V. I. Grolmusz, M. Wilmanns, B. G. Vertessy
Structural Snapshots Of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-Line Attack And Inversion
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE
    ChainsA
    EC Number3.6.1.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDUTPASE (CATALYTIC) DOMAIN, UNP RESIDUES 608-759
    GeneGAG-PRO
    MutationYES
    Organism CommonMPMV
    Organism ScientificMASON-PFIZER MONKEY VIRUS
    Organism Taxid11855

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4UMP3Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:76 , ARG A:79 , SER A:80 , GLY A:92 , VAL A:93 , ILE A:94 , ASP A:95 , TYR A:98 , GLU A:101 , ILE A:102 , LYS A:103 , MET A:105 , GLN A:123 , MG A:153 , HOH A:156 , HOH A:157 , HOH A:242 , HOH A:246BINDING SITE FOR RESIDUE UMP A 777
2AC2SOFTWAREDUP A:154 , HOH A:191 , HOH A:246 , HOH A:247 , UMP A:777BINDING SITE FOR RESIDUE MG A 153
3AC3SOFTWAREARG A:79 , SER A:80 , SER A:81 , GLY A:92 , VAL A:93 , ILE A:94 , ASP A:95 , TYR A:98 , LYS A:103 , MET A:105 , GLN A:123 , MG A:153 , HOH A:156 , HOH A:157 , HOH A:191 , HOH A:242 , HOH A:246 , HOH A:247 , HOH A:254BINDING SITE FOR RESIDUE DUP A 154
4AC4SOFTWAREGLN A:88 , VAL A:89 , TYR A:90 , PRO A:91BINDING SITE FOR RESIDUE TRS A 155

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TQ4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:66 -Pro A:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TQ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TQ4)

(-) Exons   (0, 0)

(no "Exon" information available for 3TQ4)

(-) 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:112
 aligned with O92810_MPMV | O92810 from UniProtKB/TrEMBL  Length:911

    Alignment length:112
                                   641       651       661       671       681       691       701       711       721       731       741  
          O92810_MPMV   632 KQPISKLTRATPGSAGLDLCSTSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVNNIVTVSQGNRIAQLILLPLIETDNKV 743
               SCOP domains d3tq4a_ A: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhh.........eeee....eeehhhhh.eee...ee......eeeeeeehhhhhh..eee..eee.........eeeee....eee....eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3tq4 A  25 KQPISKLTRATPGSAGLDLCSTSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVNNIVTVSQGNRIAQLILLPLIETDNKV 136
                                    34        44        54        64        74        84        94       104       114       124       134  

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TQ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TQ4)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (O92810_MPMV | O92810)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        O92810_MPMV | O928103tp1 3tpw
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        O92810_MPMV | O928103tpn 3tps 3tpy 3tq3 3tq5 3trl 3trn 3ts6 3tsl 3tta

(-) Related Entries Specified in the PDB File

2d4l 2d4m 2d4n 3tp1 3tpn 3tps 3tpw 3tpy 3tq3 3tq5 3trl 3trn 3ts6 3tsl 3tta