1SEH

Crystal structure of E. coli dUTPase complexed with the product dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase

Barabas, O.Pongracz, V.Kovari, J.Wilmanns, M.Vertessy, B.G.

(2004) J Biol Chem 279: 42907-42915

  • DOI: https://doi.org/10.1074/jbc.M406135200
  • Primary Citation of Related Structures:  
    1RN8, 1RNJ, 1SEH, 1SYL

  • PubMed Abstract: 

    dUTPase is essential to keep uracil out of DNA. Crystal structures of substrate (dUTP and alpha,beta-imino-dUTP) and product complexes of wild type and mutant dUTPases were determined to reveal how an enzyme responsible for DNA integrity functions. A kinetic analysis of wild type and mutant dUTPases was performed to obtain relevant mechanistic information in solution. Substrate hydrolysis is shown to be initiated via in-line nucleophile attack of a water molecule oriented by an activating conserved aspartate residue. Substrate binding in a catalytically competent conformation is achieved by (i) multiple interactions of the triphosphate moiety with catalysis-assisting Mg2+, (ii) a concerted motion of residues from three conserved enzyme motifs as compared with the apoenzyme, and (iii) an intricate hydrogen-bonding network that includes several water molecules in the active site. Results provide an understanding for the catalytic role of conserved residues in dUTPases.


  • Organizational Affiliation

    Institute of Enzymology, Biological Research Center, Hungarian Academy of Science, Budapest, Karolina út 29-31, H-1113, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase152Escherichia coliMutation(s): 0 
Gene Names: DUT
EC: 3.6.1.23
UniProt
Find proteins for P06968 (Escherichia coli (strain K12))
Explore P06968 
Go to UniProtKB:  P06968
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06968
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP

Download Ideal Coordinates CCD File 
B [auth A]2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.257α = 90
b = 75.257β = 90
c = 100.532γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description