1LWY

hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 

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.Mol.Biol. 10: 204-211

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

  • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
8-OXOGUANINE DNA GLYCOSYLASE
A
324Homo sapiensGene Names: OGG1 (MMH, MUTM, OGH1)
EC: 3.2.2.-, 4.2.99.18
Find proteins for O15527 (Homo sapiens)
Go to Gene View: OGG1
Go to UniProtKB:  O15527
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'D15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3'E15N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PED
Query on PED
E
NON-POLYMERC5 H13 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.032α = 90.00
b = 92.032β = 90.00
c = 211.310γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance