2ZHX

Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.234 

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This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 64: 551-560

  • DOI: 10.1107/S090744490800512X
  • Also Cited By: 4WS8, 4WS7, 4WS6, 4WS5, 4WS4, 4WS3, 4WS2, 4WS1, 4WS0, 4WRZ, 4WRY, 4WRX, 4WRW, 4WRV, 4WRU, 4WPL, 4WPK, 3A7N

  • PubMed Abstract: 
  • Uracil-DNA glycosylase (UNG), a repair enzyme involved in the excision of uracil from DNA, from mycobacteria differs from UNGs from other sources, particularly in the sequence in the catalytically important loops. The structure of the enzyme from Myc ...

    Uracil-DNA glycosylase (UNG), a repair enzyme involved in the excision of uracil from DNA, from mycobacteria differs from UNGs from other sources, particularly in the sequence in the catalytically important loops. The structure of the enzyme from Mycobacterium tuberculosis (MtUng) in complex with a proteinaceous inhibitor (Ugi) has been determined by X-ray analysis of a crystal containing seven crystallographically independent copies of the complex. This structure provides the first geometric characterization of a mycobacterial UNG. A comparison of the structure with those of other UNG proteins of known structure shows that a central core region of the molecule is relatively invariant in structure and sequence, while the N- and C-terminal tails exhibit high variability. The tails are probably important in folding and stability. The mycobacterial enzyme exhibits differences in UNG-Ugi interactions compared with those involving UNG from other sources. The MtUng-DNA complex modelled on the basis of the known structure of the complex involving the human enzyme indicates a domain closure in the enzyme when binding to DNA. The binding involves a larger burial of surface area than is observed in binding by human UNG. The DNA-binding site of MtUng is characterized by the presence of a higher proportion of arginyl residues than is found in the binding site of any other UNG of known structure. In addition to the electrostatic effects produced by the arginyl residues, the hydrogen bonds in which they are involved compensate for the loss of some interactions arising from changes in amino-acid residues, particularly in the catalytic loops. The results arising from the present investigation represent unique features of the structure and interaction of mycobacterial Ungs.


    Related Citations: 
    • 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
    • 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, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A, C, E, G, I, K, M
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase inhibitor
B, D, F, H, J, L, N
84Bacillus phage PBS2Mutation(s): 0 
Gene Names: UGI
Find proteins for P14739 (Bacillus phage PBS2)
Go to UniProtKB:  P14739
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 201.143α = 90.00
b = 64.274β = 109.72
c = 203.677γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
DENZOdata reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2018-11-21
    Type: Advisory, Data collection, Derived calculations, Source and taxonomy