1MWJ

Crystal Structure of a MUG-DNA pseudo substrate complex

• PDB DOI:  https://doi.org/10.2210/pdb1MWJ/pdb
• NAKB: 1MWJ

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-09-30 Released: 2002-10-11 
• Deposition Author(s): Barrett, T.E., Scharer, O., Savva, R., Brown, T., Jiricny, J., Verdine, G.L., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.252 
• R-Value Work: 0.190 
• R-Value Observed: 0.230 

Literature

Crystal Structure of a thwarted mismatch glycosylase DNA repair complex

Barrett, T.E., Scharer, O., Savva, R., Brown, T., Jiricny, J., Verdine, G.L., Pearl, L.H.

(1999) EMBO J 18: 6599-6609

• PubMed: 10581234 
• DOI: https://doi.org/10.1093/emboj/18.23.6599
• Primary Citation of Related Structures:  
  1MWJ


• PubMed Abstract: 
  

The bacterial mismatch-specific uracil-DNA glycosylase (MUG) and eukaryotic thymine-DNA glycosylase (TDG) enzymes form a homologous family of DNA glycosylases that initiate base-excision repair of G:U/T mismatches. Despite low sequence homology, the MUG/TDG enzymes are structurally related to the uracil-DNA glycosylase enzymes, but have a very different mechanism for substrate recognition. We have now determined the crystal structure of the Escherichia coli MUG enzyme complexed with an oligonucleotide containing a non-hydrolysable deoxyuridine analogue mismatched with guanine, providing the first structure of an intact substrate-nucleotide productively bound to a hydrolytic DNA glycosylase. The structure of this complex explains the preference for G:U over G:T mispairs, and reveals an essentially non-specific pyrimidine-binding pocket that allows MUG/TDG enzymes to excise the alkylated base, 3, N(4)-ethenocytosine. Together with structures for the free enzyme and for an abasic-DNA product complex, the MUG-substrate analogue complex reveals the conformational changes accompanying the catalytic cycle of substrate binding, base excision and product release.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.36 kDa 
• Atom Count: 1,576 
• Modelled Residue Count: 177 
• Deposited Residue Count: 180 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G/U mismatch-specific DNA glycosylase	B [auth A]	168	Escherichia coli	Mutation(s): 0  Gene Names: mug EC: 3.2.2 (PDB Primary Data), 3.2.2.28 (UniProt)
UniProt
Find proteins for P0A9H1 (Escherichia coli (strain K12)) Explore P0A9H1  Go to UniProtKB:  P0A9H1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*GP*A*GP*(DU)P*TP*CP*GP*CP*G)-3'	A [auth D]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.252 
• R-Value Work: 0.190 
• R-Value Observed: 0.230 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.996	α = 90
b = 101.996	β = 90
c = 45.133	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-11 
Deposition Author(s): Barrett, T.E., Scharer, O., Savva, R., Brown, T., Jiricny, J., Verdine, G.L., Pearl, L.H.

Revision History  

• Version 1.0: 2002-10-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description