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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1074/jbc.M406135200
  • Primary Citation of Related Structures:  
  • Also Cited By: 2HRM, 2HR6

  • 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 ...

    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.


    Related Citations: 
    • Atomic resolution structure of Escherichia coli dUTPase determined ab initio
      Gonzalez, A.,Larsson, G.,Persson, R.,Cedergren-Zeppezauer, E.
      (2001) Acta Crystallogr.,Sect.D 57: 767


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyuridine 5'-triphosphate nucleotidohydrolase
A
152Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dut (dnaS, sof)
EC: 3.6.1.23
Find proteins for P06968 (Escherichia coli (strain K12))
Go to UniProtKB:  P06968
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP

Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.257α = 90.00
b = 75.257β = 90.00
c = 100.532γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
MAR345data collection
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description