Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45786.46 
• Atom Count: 2760 
• Residue Count: 355 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2NOF

Structure of Q315F human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA

• DOI: 10.2210/pdb2NOF/pdb
• NDB: PD0893

• Classification: Hydrolase Lyase/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 2 


• Deposited: 2006-10-25 Released: 2006-11-21 
• Deposition Author(s): Radom, C.T., Banerjee, A., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 

Literature

Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations.

Radom, C.T., Banerjee, A., Verdine, G.L.

(2007) J.Biol.Chem. 282: 9182-9194

• PubMed: 17114185 
• DOI: 10.1074/jbc.M608989200
• Primary Citation of Related Structures:  
  2NOZ, 2NOL, 2NOI, 2NOH, 2NOE, 2NOB


• PubMed Abstract: 
  

The human 8-oxoguanine DNA glycosylase (hOGG1) protein is responsible for initiating base excision DNA repair of the endogenous mutagen 8-oxoguanine. Like nearly all DNA glycosylases, hOGG1 extrudes its substrate from the DNA helix and inserts it into an extrahelical enzyme active site pocket lined with residues that participate in lesion recognition and catalysis. Structural analysis has been performed on mutant versions of hOGG1 having changes in catalytic residues but not on variants having altered 7,8-dihydro-8-oxoguanine (oxoG) contact residues. Here we report high resolution structural analysis of such recognition variants. We found that Ala substitution at residues that contact the phosphate 5' to the lesion (H270A mutation) and its Watson-Crick face (Q315A mutation) simply removed key functionality from the contact interface but otherwise had no effect on structure. Ala substitution at the only residue making an oxoG-specific contact (G42A mutation) introduced torsional stress into the DNA contact surface of hOGG1, but this was overcome by local interactions within the folded protein, indicating that this oxoG recognition motif is "hardwired." Introduction of a side chain intended to sterically obstruct the active site pocket (Q315F mutation) led to two different structures, one of which (Q315F(*149)) has the oxoG lesion in an exosite flanking the active site and the other of which (Q315F(*292)) has the oxoG inserted nearly completely into the lesion recognition pocket. The latter structure offers a view of the latest stage in the base extrusion pathway yet observed, and its lack of catalytic activity demonstrates that the transition state for displacement of the lesion base is geometrically demanding.

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Organizational Affiliation: 

Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
N-glycosylase/DNA lyase	A	325	Homo sapiens	Mutation(s): 2  Gene Names: OGG1 (MMH, MUTM, OGH1)
Find proteins for O15527 (Homo sapiens) Go to Gene View: OGG1 Go to UniProtKB:  O15527

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'	B	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*GP*CP*GP*TP*C*CP*AP*(G42)P*GP*TP*CP*TP*AP*CP*C)-3'	C	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
8OG	C	DNA LINKING	C10 H14 N5 O8 P		DG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 92.267	α = 90.00
b = 92.267	β = 90.00
c = 211.128	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing
CBASS	data collection
DENZO	data reduction
PDB_EXTRACT	data extraction
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-25 
• Released Date: 2006-11-21 
• Deposition Author(s): Radom, C.T., Banerjee, A., Verdine, G.L.

Revision History 

• Version 1.0: 2006-11-21
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-18
  Type: Refinement description