1M3Q

Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase

Chung, S.J.Verdine, G.L.

(2004) Chem Biol 11: 1643-1649

  • DOI: 10.1016/j.chembiol.2004.09.014
  • Primary Citation of Related Structures:  
    1M3H, 1M3Q

  • PubMed Abstract: 
  • DNA glycosylase/lyases initiate the repair of damaged nucleobases in the genome by catalyzing excision of aberrant nucleobases and nicking of the lesion-containing DNA strand. Nearly all of these proteins have the unusual property of remaining tightl ...

    DNA glycosylase/lyases initiate the repair of damaged nucleobases in the genome by catalyzing excision of aberrant nucleobases and nicking of the lesion-containing DNA strand. Nearly all of these proteins have the unusual property of remaining tightly bound in vitro to the end products of the reaction cascade. We have taken advantage of this property to crystallize and structurally characterize the end product resulting from complete DNA processing by a catalytically active mutant form of human 8-oxoguanine DNA glycosylase (D268E hOgg1). The resulting structure is consistent with the currently accepted catalytic mechanism for the protein. Unexpectedly, however, soaking of a nucleobase analog into the crystals results in religation of the DNA backbone in situ.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
8-oxoguanine DNA glycosylaseA317Homo sapiensMutation(s): 1 
Gene Names: OGG1MMHMUTMOGH1
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (UniProt)
Find proteins for O15527 (Homo sapiens)
Explore O15527 
Go to UniProtKB:  O15527
NIH Common Fund Data Resources
PHAROS  O15527
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3'C15N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'B15N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ANG
      Query on ANG

      Download CCD File 
      A
      8-AMINOGUANINE
      C5 H6 N6 O
      WYDKPTZGVLTYPG-UHFFFAOYSA-N
       Ligand Interaction
      CA
      Query on CA

      Download CCD File 
      C
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.90 Å
      • R-Value Free: 0.268 
      • R-Value Work: 0.235 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 92.415α = 90
      b = 92.415β = 90
      c = 211.425γ = 120
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-02-17
        Type: Initial release
      • Version 1.1: 2008-04-28
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance