1M3Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 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

  • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
8-oxoguanine DNA glycosylase
A
317Homo 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'B15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3'C15N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ANG
Query on ANG

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Download CCD File 
A
8-AMINOGUANINE
C5 H6 N6 O
WYDKPTZGVLTYPG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DRZ
Query on DRZ
C
DNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 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 = 90.00
b = 92.415β = 90.00
c = 211.425γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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