Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

Starting Model: experimental
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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: https://doi.org/10.1016/j.jmb.2004.06.028
  • Primary Citation of Related Structures:  
    1MQ7, 1SIX, 1SJN, 1SLH, 1SM8, 1SMC, 1SNF

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase
A, B, C
174Mycobacterium tuberculosisMutation(s): 0 
Gene Names: DUTRV2697CMT2771MTCY05A6.18CMB2716C
Find proteins for P9WNS5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNS5 
Go to UniProtKB:  P9WNS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNS5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DUD

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
K [auth C]
C9 H14 N2 O11 P2
Query on TRS

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
C4 H12 N O3
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
J [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.273α = 90
b = 108.273β = 90
c = 100.792γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description