1M3H

Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

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 tightly bo ...

    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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
8-Oxoguanine DNA Glycosylase A317Homo 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
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'B15N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(P*GP*CP*GP*TP*CP*CP*AP*(DDX))-3'C8N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*TP*CP*TP*AP*CP*C)-3'D7N/A
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        CA
        Query on CA

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

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.05 Å
        • R-Value Free: 0.282 
        • R-Value Work: 0.239 
        • R-Value Observed: 0.239 
        • Space Group: P 65 2 2
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 92.345α = 90
        b = 92.345β = 90
        c = 211.345γ = 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: 2004-04-20
          Type: Initial release
        • Version 1.1: 2008-04-28
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance