1WEI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M403944200
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A/G-specific adenine glycosylase
A
225Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: mutY (micA)
EC: 3.2.2.31
Find proteins for P17802 (Escherichia coli (strain K12))
Go to UniProtKB:  P17802
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 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
ADE
Query on ADE

Download SDF File 
Download CCD File 
A
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADEKd: ~1 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.502α = 90.00
b = 49.325β = 122.59
c = 69.609γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance