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(-) Description

Title :  DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)
 
Authors :  G. Larsson, L. A. Svensson, P. O. Nyman
Date :  30 Apr 96  (Deposition) - 08 Nov 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Hydrolase, Nucleotide Metabolism, D-Utpase, Substrate Analogue, D-Udp Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Larsson, L. A. Svensson, P. O. Nyman
Crystal Structure Of The Escherichia Coli Dutpase In Comple With A Substrate Analogue (Dudp).
Nat. Struct. Biol. V. 3 532 1996
PubMed-ID: 8646539  |  Reference-DOI: 10.1038/NSB0696-532

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A
    EC Number: 3.6.1.23
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1DUD1Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1DUD3Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:68 , SER A:72 , GLY A:73 , ASN A:84 , GLY A:87 , LEU A:88 , ILE A:89 , ASP A:90 , TYR A:93 , GLN A:96 , MET A:98 , GLN A:119 , HOH A:235 , HOH A:271 , HOH A:359 , HOH A:390 , HOH A:392BINDING SITE FOR RESIDUE DUD A 153

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DUD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DUD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DUD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DUD)

(-) Exons   (0, 0)

(no "Exon" information available for 1DUD)

(-) Sequences/Alignments

Asymmetric Unit
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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:136
 aligned with DUT_ECOLI | P06968 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:136
                             1                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129      
            DUT_ECOLI     - -MKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDF 135
               SCOP domains d1duda_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                    SCOP domains
               CATH domains 1dudA00 A:1-136  [code=2.70.40.10, no name defined]                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....................eeeee.....eee...eeeeeeeeeeee....eeeeeee..hhhhhhheeeee...eee.......eeeeeeee....eee..eeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dud A   1 MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDF 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
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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  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DUD)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (DUT_ECOLI | P06968)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006226    dUMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0046081    dUTP catabolic process    The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.
    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).
    GO:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_ECOLI | P06968: 1dup 1eu5 1euw 1rn8 1rnj 1seh 1syl 2hr6 2hrm

(-) Related Entries Specified in the PDB File

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