Catalytic Domain Of Muty From Escherichia Coli K20A Mutant Complexed To Adenine

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

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Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase

Manuel, R.C.Hitomi, K.Arvai, A.S.House, P.G.Kurtz, A.J.Dodson, M.L.McCullough, A.K.Tainer, J.A.Lloyd, R.S.

(2004) J Biol Chem 279: 46930-46939

  • DOI: https://doi.org/10.1074/jbc.M403944200
  • Primary Citation of Related Structures:  
    1WEF, 1WEG, 1WEI

  • PubMed Abstract: 

    The Escherichia coli adenine DNA glycosylase, MutY, plays an important role in the maintenance of genomic stability by catalyzing the removal of adenine opposite 8-oxo-7,8-dihydroguanine or guanine in duplex DNA. Although the x-ray crystal structure of the catalytic domain of MutY revealed a mechanism for catalysis of the glycosyl bond, it appeared that several opportunistically positioned lysine side chains could participate in a secondary beta-elimination reaction. In this investigation, it is established via site-directed mutagenesis and the determination of a 1.35-A structure of MutY in complex with adenine that the abasic site (apurinic/apyrimidinic) lyase activity is alternatively regulated by two lysines, Lys142 and Lys20. Analyses of the crystallographic structure also suggest a role for Glu161 in the apurinic/apyrimidinic lyase chemistry. The beta-elimination reaction is structurally and chemically uncoupled from the initial glycosyl bond scission, indicating that this reaction occurs as a consequence of active site plasticity and slow dissociation of the product complex. MutY with either the K142A or K20A mutation still catalyzes beta and beta-delta elimination reactions, and both mutants can be trapped as covalent enzyme-DNA intermediates by chemical reduction. The trapping was observed to occur both pre- and post-phosphodiester bond scission, establishing that both of these intermediates have significant half-lives. Thus, the final spectrum of DNA products generated reflects the outcome of a delicate balance of closely related equilibrium constants.

  • Organizational Affiliation

    Sealy Center for Molecular Science and Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas 77555-1071, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A/G-specific adenine glycosylase225Escherichia coliMutation(s): 1 
EC: 3.2.2 (PDB Primary Data), (UniProt)
Find proteins for P17802 (Escherichia coli (strain K12))
Explore P17802 
Go to UniProtKB:  P17802
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17802
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.502α = 90
b = 49.325β = 122.59
c = 69.609γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-08-28
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2021-11-10
    Changes: Database references, Derived calculations