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 
  • R-Value Observed: 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:  
    1R2Z, 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:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MutMA274Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mutMfpg
EC: 3.2.2.23 (UniProt), 4.2.99.18 (UniProt)
Find proteins for P84131 (Geobacillus stearothermophilus)
Explore P84131 
Go to UniProtKB:  P84131
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'B12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      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 CCD File 
      A
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.63 Å
      • R-Value Free: 0.233 
      • R-Value Work: 0.208 
      • R-Value Observed: 0.208 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 44.591α = 90
      b = 94.226β = 90
      c = 102.18γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      HKL-2000data reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

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