2PY4

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor.

Varga, B.Barabas, O.Takacs, E.Nagy, N.Nagy, P.Vertessy, B.G.

(2008) Biochem Biophys Res Commun 373: 8-13

  • DOI: https://doi.org/10.1016/j.bbrc.2008.05.130
  • Primary Citation of Related Structures:  
    2PY4

  • PubMed Abstract: 

    dUTPases are essential to eliminate dUTP for DNA integrity and provide dUMP for thymidylate biosynthesis. Mycobacterium tuberculosis apparently lacks any other thymidylate biosynthesis pathway, therefore dUTPase is a promising antituberculotic drug target. Crystal structure of the mycobacterial enzyme in complex with the isosteric substrate analog, alpha,beta-imido-dUTP and Mg(2+) at 1.5A resolution was determined that visualizes the full-length C-terminus, previously not localized. Interactions of a conserved motif important in catalysis, the Mycobacterium-specific five-residue-loop insert and C-terminal tetrapeptide could now be described in detail. Stacking of C-terminal histidine upon the uracil moiety prompted replacement with tryptophan. The resulting sensitive fluorescent sensor enables fast screening for binding of potential inhibitors to the active site. K(d) for alpha,beta-imido-dUTP binding to mycobacterial dUTPase is determined to be 10-fold less than for human dUTPase, which is to be considered in drug optimization. A robust continuous activity assay for kinetic screening is proposed.


  • Organizational Affiliation

    Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Hungarian Academy of Sciences, Karolina ut 29, H-1113 Budapest, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase174Mycobacterium tuberculosisMutation(s): 0 
Gene Names: dut
EC: 3.6.1.23
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

Download Ideal Coordinates CCD File 
C [auth A]2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DUP Binding MOAD:  2PY4 Kd: 200 (nM) from 1 assay(s)
PDBBind:  2PY4 Kd: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.591α = 90
b = 54.591β = 90
c = 83.051γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
STARTdata collection
XDSdata reduction
XSCALEdata 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: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description