1MQ7

CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.

Chan, S.Segelke, B.Lekin, T.Krupka, H.Cho, U.S.Kim, M.-Y.So, M.Kim, C.-Y.Naranjo, C.M.Rogers, Y.C.Park, M.S.Waldo, G.S.Pashkov, I.Cascio, D.Perry, J.L.Sawaya, M.R.

(2004) J.Mol.Biol. 341: 503-517

  • DOI: 10.1016/j.jmb.2004.06.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essenti ...

    The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.


    Related Citations: 
    • HUMAN DUTP PYROPHOSPHATASE: URACIL RECOGNITION BY A BETA HAIRPIN AND ACTIVE SITES FORMED BY THREE SEPARATE SUBUNITS
      Mol, C.D.,Harris, J.M.,Mclntosh, E.M.,Tainer, J.A.
      (1996) STRUCTURE 4: 1077


    Organizational Affiliation

    UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, 206 Boyer Hall, Box 951570, Los Angeles, CA 90095-1570, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
A
154Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: dut
EC: 3.6.1.23
Find proteins for P9WNS5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNS5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 98.823α = 90.00
b = 98.823β = 90.00
c = 98.823γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
EPMRphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-09
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance