Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.7 kDa 
• Atom Count: 3,069 
• Modelled Residue Count: 339 
• Deposited Residue Count: 344 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1YQM

Catalytically inactive human 8-oxoguanine glycosylase crosslinked to 7-deazaguanine containing DNA

• PDB DOI: 10.2210/pdb1YQM/pdb
• NDB: PD0631

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-02-02 Released: 2005-04-05 
• Deposition Author(s): Banerjee, A., Yang, W., Karplus, M., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

Banerjee, A., Yang, W., Karplus, M., Verdine, G.L.

(2005) Nature 434: 612-618

• PubMed: 15800616 
• DOI: 10.1038/nature03458
• Primary Citation of Related Structures:  
  1YQK, 1YQL, 1YQM, 1YQR


• PubMed Abstract: 
  

How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	C [auth A]	319	Homo sapiens	Mutation(s): 2  Gene Names: OGG1, MMH, MUTM, OGH1 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15527 (Homo sapiens) Explore O15527  Go to UniProtKB:  O15527
PHAROS:  O15527

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*C)-3'	A [auth B]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*TP*CP*CP*AP*(7GU)P*GP*TP*CP*TP*AP*C)-3'	B [auth C]	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth C], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.508	α = 90
b = 92.508	β = 90
c = 210.649	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-05 
Deposition Author(s): Banerjee, A., Yang, W., Karplus, M., Verdine, G.L.

Revision History  

• Version 1.0: 2005-04-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations