4WS7

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-chlorouracil, Form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications.

Arif, S.M.Geethanandan, K.Mishra, P.Surolia, A.Varshney, U.Vijayan, M.

(2015) Acta Crystallogr.,Sect.D 71: 1514-1527

  • DOI: 10.1107/S1399004715009311
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic paramet ...

    17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5' position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.


    Related Citations: 
    • Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands.
      Kaushal, P.S.,Talawar, R.K.,Varshney, U.,Vijayan, M.
      (2010) Acta Crystallogr.,Sect.F 66: 887
    • Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.
      Kaushal, P.S.,Talawar, R.K.,Krishna, P.D.,Varshney, U.,Vijayan, M.
      (2008) Acta Crystallogr.,Sect.D 64: 551
    • X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG.
      Ravishankar, R.,Bidya Sagar, M.,Roy, S.,Purnapatre, K.,Handa, P.,Varshney, U.,Vijayan, M.
      (1998) Nucleic Acids Res. 26: 4880
    • Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.
      Saikrishnan, K.,Bidya Sagar, M.,Ravishankar, R.,Roy, S.,Purnapatre, K.,Handa, P.,Varshney, U.,Vijayan, M.
      (2002) Acta Crystallogr.,Sect.D 58: 1269


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A
238Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ung
EC: 3.2.2.27
Find proteins for P9WFQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WFQ9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
5UC
Query on 5UC

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Download CCD File 
A
5-chloropyrimidine-2,4(1H,3H)-dione
C4 H3 Cl N2 O2
ZFTBZKVVGZNMJR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.142 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.370α = 90.00
b = 43.780β = 98.46
c = 67.230γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Advisory, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary