1MWI | pdb_00001mwi

Crystal structure of a MUG-DNA product complex

• PDB DOI: https://doi.org/10.2210/pdb1MWI/pdb
• NAKB: 1MWI

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


• Deposited: 2002-09-30 Released: 2002-10-04 
• Deposition Author(s): Barrett, T.E., Savva, R., Panayotou, G., Brown, T., Barlow, T., Jiricny, J., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions.

Barrett, T.E., Savva, R., Panayotou, G., Barlow, T., Brown, T., Jiricny, J., Pearl, L.H.

(1998) Cell 92: 117-129

• PubMed: 9489705 
• DOI: https://doi.org/10.1016/s0092-8674(00)80904-6
• Primary Citation Related Structures: 
  1MUG, 1MWI


• PubMed Abstract: 
  

  G:U mismatches resulting from deamination of cytosine are the most common promutagenic lesions occurring in DNA. Uracil is removed in a base-excision repair pathway by uracil DNA-glycosylase (UDG), which excises uracil from both single- and double-stranded DNA. Recently, a biochemically distinct family of DNA repair enzymes has been identified, which excises both uracil and thymine, but only from mispairs with guanine. Crystal structures of the mismatch-specific uracil DNA-glycosylase (MUG) from E. coli, and of a DNA complex, reveal a remarkable structural and functional homology to UDGs despite low sequence identity. Details of the MUG structure explain its thymine DNA-glycosylase activity and the specificity for G:U/T mispairs, which derives from direct recognition of guanine on the complementary strand.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University College London, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.27 kDa 
• Atom Count: 1,629 
• Modeled 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*AP*GP*(AAB)P*TP*CP*GP*CP*G)-3'	A [auth D]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.35	α = 90
b = 101.35	β = 90
c = 45.01	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: 2002-10-04 
Deposition Author(s): Barrett, T.E., Savva, R., Panayotou, G., Brown, T., Barlow, T., Jiricny, J., Pearl, L.H.

Revision History  

• Version 1.0: 2002-10-04
  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: 2014-07-09
  Changes: Non-polymer description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description