3A7N

Crystal structure of uracil-DNA glycosylase from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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 Struct Biol Cryst Commun 66: 887-892

  • DOI: 10.1107/S1744309110023043
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is ...

    Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from other sources. However, differences exist in the N- and C-terminal stretches and some catalytic loops. Comparison with appropriate structures indicate that the two-domain enzyme closes slightly when binding to DNA, while it opens slightly when binding to the proteinaceous inhibitor Ugi. The structural changes in the catalytic loops on complexation reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino-acid residues in the catalytic loops. The uracil-binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil, in addition to providing insights into other possible interactions that inhibitors could be involved in.


    Related Citations: 
    • 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.V., Varshney, U., Vijayan, M.
      (2008) Acta Crystallogr D Biol Crystallogr 64: 551
    • 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 D Biol Crystallogr 58: 1269
    • 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

    Organizational Affiliation

    Molecular Biophysics Unit, 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 glycosylaseA238Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ungRv2976cMTCY349.11
EC: 3.2.2.3 (PDB Primary Data), 3.2.2.27 (UniProt)
Find proteins for P9WFQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFQ9 
Go to UniProtKB:  P9WFQ9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.84α = 90
b = 63.67β = 90
c = 86.4γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance