4O9M

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1038/nsmb.2818
  • Primary Citation of 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.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase betaD [auth A]335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
GTEx:  ENSG00000070501 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06746
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')A [auth B]16N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')B [auth C]11N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
(5'-D(P*GP*TP*CP*GP*G)-3');C [auth D]5N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2RW
Query on 2RW
Download Ideal Coordinates CCD File 
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
Query on NA
Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.627α = 90
b = 78.873β = 105.94
c = 54.324γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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