1R2Z

MutM (Fpg) bound to 5,6-dihydrouracil (DHU) containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM.

Fromme, J.C.Verdine, G.L.

(2003) J.Biol.Chem. 278: 51543-51548

  • DOI: 10.1074/jbc.M307768200
  • Primary Citation of Related Structures:  1R2Y

  • PubMed Abstract: 
  • MutM is a bacterial DNA glycosylase that removes the mutagenic lesion 8-oxoguanine (oxoG) from duplex DNA. The means of oxoG recognition by MutM (also known as Fpg) is of fundamental interest, in light of the vast excess of normal guanine bases prese ...

    MutM is a bacterial DNA glycosylase that removes the mutagenic lesion 8-oxoguanine (oxoG) from duplex DNA. The means of oxoG recognition by MutM (also known as Fpg) is of fundamental interest, in light of the vast excess of normal guanine bases present in genomic DNA. The crystal structure of a recognition-competent but catalytically inactive version of MutM in complex with oxoG-containing DNA reveals the structural basis for recognition. MutM binds the oxoG nucleoside in the syn glycosidic configuration and distinguishes oxoG from guanine by reading out the protonation state of the N7 atom. The segment of MutM principally responsible for oxoG recognition is a flexible loop, suggesting that conformational mobility influences lesion recognition and catalysis. Furthermore, the structure of MutM in complex with DNA containing an alternative substrate, dihydrouracil, demonstrates how MutM is able to recognize lesions other than oxoG.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MutM
A
274Geobacillus stearothermophilusGene Names: mutM (fpg)
EC: 3.2.2.23
Find proteins for P84131 (Geobacillus stearothermophilus)
Go to UniProtKB:  P84131
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'B12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*CP*GP*TP*CP*CP*AP*(DHU)P*GP*TP*CP*TP*AP*CP*C)-3'C12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UMP
Query on UMP
C
NON-POLYMERC9 H13 N2 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.591α = 90.00
b = 94.226β = 90.00
c = 102.180γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance