4O9M | pdb_00004o9m

Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA

• PDB DOI: https://doi.org/10.2210/pdb4O9M/pdb
• NAKB: 4O9M

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-02 Released: 2014-04-30 
• Deposition Author(s): Caglayan, M., Batra, V.K., Sassa, A., Prasad, R., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Role of polymerase beta in complementing aprataxin deficiency during abasic-site base excision repair.

Caglayan, M., Batra, V.K., Sassa, A., Prasad, R., Wilson, S.H.

(2014) Nat Struct Mol Biol 21: 497-499

• PubMed: 24777061 
• DOI: https://doi.org/10.1038/nsmb.2818
• Primary Citation Related Structures: 
  4O9M


• PubMed Abstract: 
  

  DNA polymerase β (pol β) lyase removal of 5'-deoxyribose phosphate (5'-dRP) from base excision repair (BER) intermediates is critical in mammalian BER involving the abasic site. We found that pol β also removes 5'-adenylated dRP from BER intermediates after abortive ligation. The crystal structure of a human pol β-DNA complex showed the 5'-AMP-dRP group positioned in the lyase active site. Pol β expression rescued methyl methanesulfonate sensitivity in aprataxin (hnt3)- and FEN1 (rad27)-deficient yeast.

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Organizational Affiliation: 
• Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.55 kDa 
• Atom Count: 3,599 
• Modeled Residue Count: 358 
• Deposited Residue Count: 367 
• Unique protein chains: 1
• Unique nucleic acid chains: 2
• Unique hybrid chains: 1

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	D [auth A]	335	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746  Go to UniProtKB:  P06746
PHAROS:  P06746 GTEx:  ENSG00000070501

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	A [auth B]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')	B [auth C]	11	N/A

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2RW	E [auth D]	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate C15 H23 N5 O12 P2 ZJGNPGFGXQKXSY-IBCGMDAMSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.627	α = 90
b = 78.873	β = 105.94
c = 54.324	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Caglayan, M., Batra, V.K., Sassa, A., Prasad, R., Wilson, S.H.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description