1HU0

CRYSTAL STRUCTURE OF AN HOGG1-DNA BOROHYDRIDE TRAPPED INTERMEDIATE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Product-Assisted Catalysis in base-excision DNA Repair

Fromme, J.C.Bruner, S.D.Yang, W.Karplus, M.Verdine, G.L.

(2003) Nat Struct Biol 10: 204-211

  • DOI: 10.1038/nsb902
  • Primary Citation of Related Structures:  
    1HU0, 1LWY, 1LWW, 1LWV

  • PubMed Abstract: 
  • Most spontaneous damage to bases in DNA is corrected through the action of the base-excision DNA repair pathway. Base excision repair is initiated by DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in DNA and catalyze their ex ...

    Most spontaneous damage to bases in DNA is corrected through the action of the base-excision DNA repair pathway. Base excision repair is initiated by DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in DNA and catalyze their excision. How such proteins accomplish the feat of catalyzing no fewer than five sequential reaction steps using a single active site has been unknown. To help answer this, we report the structure of a trapped catalytic intermediate in DNA repair by human 8-oxoguanine DNA glycosylase. This structure and supporting biochemical results reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an enzyme-catalyzed reaction.


    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
8-OXOGUANINE DNA GLYCOSYLASE 1A324Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
  • 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'D15N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3'E15N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      OXG
      Query on OXG

      Download CCD File 
      A
      8-OXOGUANINE
      C5 H3 N5 O2
      UBKVUFQGVWHZIR-UHFFFAOYSA-N
       Ligand Interaction
      CA
      Query on CA

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.35 Å
      • R-Value Free: 0.245 
      • R-Value Work: 0.210 
      • R-Value Observed: 0.210 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 91.988α = 90
      b = 91.988β = 90
      c = 211.615γ = 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: 2003-02-25
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance