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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47769.85 
• Atom Count: 3245 
• Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

3RJJ

Ternary complex crystal structure of DNA Polymerase Beta with template 8odG provides insight into mutagenic lesion bypass

• DOI: 10.2210/pdb3RJJ/pdb
• NDB: NA1083

• Classification: Transferase Lyase/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2011-04-15 Released: 2012-01-18 
• Deposition Author(s): Batra, V.K., Beard, W.A., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.261 
• R-Value Work: 0.202 

Literature

Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion.

Batra, V.K., Shock, D.D., Beard, W.A., McKenna, C.E., Wilson, S.H.

(2012) Proc.Natl.Acad.Sci.USA 109: 113-118

• PubMed: 22178760 
• DOI: 10.1073/pnas.1112235108
• Primary Citation of Related Structures:  
  3RJK, 3RJI, 3RJH, 3RJG, 3RJF, 3RJE


• PubMed Abstract: 
  

Oxidation of genomic DNA forms the guanine lesion 7,8-dihydro-8-oxoguanine (8-oxoG). When in the template base position during DNA synthesis the 8-oxoG lesion has dual coding potential by virtue of its anti- and syn-conformations, base pairing with cytosine and adenine, respectively. This impacts mutagenesis, because insertion of adenine opposite template 8-oxoG can result in a G to T transversion. DNA polymerases vary by orders of magnitude in their preferences for mutagenic vs. error-free 8-oxoG lesion bypass. Yet, the structural basis for lesion bypass specificity is not well understood. The DNA base excision repair enzyme DNA polymerase (pol) β is presented with gap-filling synthesis opposite 8-oxoG during repair and has similar insertion efficiencies for dCTP and dATP. We report the structure of pol β in binary complex with template 8-oxoG in a base excision repair substrate. The structure reveals both the syn- and anti-conformations of template 8-oxoG in the confines of the polymerase active site, consistent with the dual coding observed kinetically for this enzyme. A ternary complex structure of pol β with the syn-8-oxoG:anti-A Hoogsteen base pair in the closed fully assembled preinsertion active site is also reported. The syn-conformation of 8-oxoG is stabilized by minor groove hydrogen bonding between the side chain of Arg283 and O8 of 8-oxoG. An adjustment in the position of the phosphodiester backbone 5'-phosphate enables 8-oxoG to adopt the syn-conformation.

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Organizational Affiliation: 

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase beta	A	335	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens) Go to Gene View: POLB Go to UniProtKB:  P06746

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	T	16	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')	P	10	N/A

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (5'-D(P*GP*TP*CP*GP*G)-3')	D	5	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.261 
• R-Value Work: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 54.480	α = 90.00
b = 79.410	β = 105.51
c = 54.910	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-15 
• Released Date: 2012-01-18 
• Deposition Author(s): Batra, V.K., Beard, W.A., Wilson, S.H.

Revision History 

• Version 1.0: 2012-01-18
  Type: Initial release