4CIS

Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Ribose-protonated DNA base excision repair: a combined theoretical and experimental study.

Sadeghian, K.Flaig, D.Blank, I.D.Schneider, S.Strasser, R.Stathis, D.Winnacker, M.Carell, T.Ochsenfeld, C.

(2014) Angew. Chem. Int. Ed. Engl. 53: 10044-10048

  • DOI: 10.1002/anie.201403334

  • PubMed Abstract: 
  • Living organisms protect the genome against external influences by recognizing and repairing damaged DNA. A common source of gene mutation is the oxidized guanine, which undergoes base excision repair through cleavage of the glycosidic bond between t ...

    Living organisms protect the genome against external influences by recognizing and repairing damaged DNA. A common source of gene mutation is the oxidized guanine, which undergoes base excision repair through cleavage of the glycosidic bond between the ribose and the nucleobase of the lesion. We unravel the repair mechanism utilized by bacterial glycosylase, MutM, using quantum-chemical calculations involving more than 1000 atoms of the catalytic site. In contrast to the base-protonated pathway currently favored in the literature, we show that the initial protonation of the lesion's ribose paves the way for an almost barrier-free glycosidic cleavage. The combination of theoretical and experimental data provides further insight into the selectivity and discrimination of MutM's binding site toward various substrates.


    Organizational Affiliation

    Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, 81377 Munich (Germany); Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, 81377 Munich (Germany).




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FORMAMIDOPYRIMIDIN DNA GLYCOSYLASE
A, B
283Lactococcus lactis subsp. cremoris (strain SK11)Mutation(s): 0 
Gene Names: mutM (fpg)
EC: 3.2.2.23
Find proteins for Q031W6 (Lactococcus lactis subsp. cremoris (strain SK11))
Go to UniProtKB:  Q031W6
Entity ID: 2
MoleculeChainsLengthOrganism
DNAC14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNAD14synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BU3
Query on BU3

Download SDF File 
Download CCD File 
A
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
68Z
Query on 68Z
D
DNA LINKINGC11 H16 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.063α = 90.00
b = 112.692β = 90.00
c = 132.882γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references
  • Version 1.2: 2014-09-17
    Type: Database references
  • Version 2.0: 2018-03-07
    Type: Atomic model, Database references, Source and taxonomy