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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI DUTPASE COMPLEXED WITH THE PRODUCT DUMP
 
Authors :  O. Barabas, J. Kovari, V. Pongracz, M. Wilmanns, B. G. Vertessy
Date :  17 Feb 04  (Deposition) - 07 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  A  (6x)
Keywords :  Enzyme-Ligand Complex, Jelly Roll, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Barabas, V. Pongracz, J. Kovari, M. Wilmanns, B. G. Vertessy
Structural Insights Into The Catalytic Mechanism Of Phosphate Ester Hydrolysis By Dutpase
J. Biol. Chem. V. 279 42907 2004
PubMed-ID: 15208312  |  Reference-DOI: 10.1074/JBC.M406135200
(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 BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DUT
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A
Biological Unit 2 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2UMP3Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2UMP6Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:68 , SER A:72 , ASN A:84 , GLY A:87 , LEU A:88 , ILE A:89 , ASP A:90 , TYR A:93 , LEU A:97 , MET A:98 , ARG A:141 , HOH A:779 , HOH A:797 , HOH A:851 , HOH A:870BINDING SITE FOR RESIDUE UMP A 777
2AC2SOFTWARETRP A:102 , ARG A:104 , HOH A:822 , HOH A:830BINDING SITE FOR RESIDUE TRS A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SEH)

(-) 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:140
 aligned with DUT_ECOLI | P06968 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:141
                             1                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139 
            DUT_ECOLI     - -MKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDATDR 140
               SCOP domains d1seha_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                         SCOP domains
               CATH domains 1sehA00 A:1-141  [code=2.70.40.10, no name defined]                                                                                           CATH domains
               Pfam domains ---------------dUTPase-1sehA01 A:16-141                                                                                                       Pfam domains
         Sec.struct. author .....eeee.....................eeee......eee....eeeeeeeeeee.....eeeeee.hhhhhhhhheee....eee......eeeeeeee.....eee....eeeeeeeee...............-. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1seh A   1 MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDAT-R 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-|
                                                                                                                                                                    139 |
                                                                                                                                                                      141
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: dUTPase (38)

(-) 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: 1dud 1dup 1eu5 1euw 1rn8 1rnj 1syl 2hr6 2hrm

(-) Related Entries Specified in the PDB File

1rn8 DUTPASE COMPLEXED WITH SUBSTRATE ANALOGUE IMIDO-DUTP
1rnj INACTIVE MUTANT DUTPASE COMPLEXED WITH SUBSTRATE ANALOGUE IMIDO-DUTP
1ro1 DUTPASE COMPLEXED WITH THE HIGH-ENERGY INTERMEDIATE ALFA, BETA-AMINOPHOSPHORANE-DUTP
1syl INACTIVE MUTANT DUTPASE COMPLEXED WITH SUBSTRATE DUTP