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: 47650.72 
• Atom Count: 3263 
• Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

3ISC

Binary complex of human DNA polymerase beta with an abasic site (THF) in the gapped DNA

• DOI: 10.2210/pdb3ISC/pdb
• NDB: NA0131

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2009-08-25 Released: 2009-09-15 
• Deposition Author(s): Beard, W.A., Shock, D.D., Batra, V.K., Pedersen, L.C., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 

Literature

DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".

Beard, W.A., Shock, D.D., Batra, V.K., Pedersen, L.C., Wilson, S.H.

(2009) J.Biol.Chem. 284: 31680-31689

• PubMed: 19759017 
• DOI: 10.1074/jbc.M109.029843
• Primary Citation of Related Structures:  
  3ISD, 3ISB


• PubMed Abstract: 
  

Apurinic/apyrimidinic (AP) sites are continuously generated in genomic DNA. Left unrepaired, AP sites represent noninstructional premutagenic lesions that are impediments to DNA synthesis. When DNA polymerases encounter an AP site, they generally insert dAMP. This preferential insertion is referred to as the A-rule. Crystallographic structures of DNA polymerase (pol) beta, a family X polymerase, with active site mismatched nascent base pairs indicate that the templating (i.e. coding) base is repositioned outside of the template binding pocket thereby diminishing interactions with the incorrect incoming nucleotide. This effectively produces an abasic site because the template pocket is devoid of an instructional base. However, the template pocket is not empty; an arginine residue (Arg-283) occupies the space vacated by the templating nucleotide. In this study, we analyze the kinetics of pol beta insertion opposite an AP site and show that the preferential incorporation of dAMP is lost with the R283A mutant. The crystallographic structures of pol beta bound to gapped DNA with an AP site analog (tertrahydrofuran) in the gap (binary complex) and with an incoming nonhydrolyzable dATP analog (ternary complex) were solved. These structures reveal that binding of the dATP analog induces a closed polymerase conformation, an unstable primer terminus, and an upstream shift of the templating residue even in the absence of a template base. Thus, dATP insertion opposite an abasic site and dATP misinsertions have common features.

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Organizational Affiliation: 

Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, 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
5'-D(P*GP*TP*CP*GP*G)-3'	D	5	N/A

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

Entity ID: 4
Molecule	Chains	Length	Organism
5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'	T	16	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
3DR	T	DNA LINKING	C5 H11 O6 P		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 54.410	α = 90.00
b = 79.300	β = 105.80
c = 54.950	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-25 
• Released Date: 2009-09-15 
• Deposition Author(s): Beard, W.A., Shock, D.D., Batra, V.K., Pedersen, L.C., Wilson, S.H.

Revision History 

• Version 1.0: 2009-09-15
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance