Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.33 kDa 
• Atom Count: 3363 
• Residue Count: 359 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

2P66

Human DNA Polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA

• DOI: 10.2210/pdb2P66/pdb
• NDB: PD0983

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


• Deposited: 2007-03-16 Released: 2007-04-10 
• Deposition Author(s): Prasad, R., Batra, V.K., Yang, X.-P., Krahn, J.M., Pedersen, L.C., Beard, W.A., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.280 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Structural insight into the DNA Polymerase beta deoxyribose phosphate lyase mechanism

Prasad, R., Batra, V.K., Yang, X.-P., Krahn, J.M., Pedersen, L.C., Beard, W.A., Wilson, S.H.

(2005) DNA Repair (Amst) 4: 1347-1357

• PubMed: 16172026 
• DOI: 10.1016/j.dnarep.2005.08.009
• Structures With Same Primary Citation


• PubMed Abstract: 
  

A large number of biochemical and genetic studies have demonstrated the involvement of DNA polymerase beta (Pol beta) in mammalian base excision repair (BER). Pol beta participates in BER sub-pathways by contributing gap filling DNA synthesis and lyase removal of the 5'-deoxyribose phosphate (dRP) group from the cleaved abasic site. To better understand the mechanism of the dRP lyase reaction at an atomic level, we determined a crystal structure of Pol beta complexed with 5'-phosphorylated abasic sugar analogs in nicked DNA. This DNA ligand represents a potential BER intermediate. The crystal structure reveals that the dRP group is bound in a non-catalytic binding site. The catalytic nucleophile in the dRP lyase reaction, Lys72, and all other potential secondary nucleophiles, are too far away to participate in nucleophilic attack on the C1' of the sugar. An approximate model of the dRP group in the expected catalytic binding site suggests that a rotation of 120 degrees about the dRP 3'-phosphate is required to position the epsilon-amino Lys72 close to the dRP C1'. This model also suggests that several other side chains are in position to facilitate the beta-elimination reaction. From results of mutational analysis of key residues in the dRP lyase active site, it appears that the substrate dRP can be stabilized in the observed non-catalytic binding conformation, hindering dRP lyase activity.

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Organizational Affiliation: 

Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.

Macromolecules

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

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

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

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(P*(3DR)P*GP*TP*CP*GP*G)-3')	D	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	A, C	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.280 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.7	α = 90
b = 81.1	β = 108.6
c = 54.9	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-16 
• Released Date: 2007-04-10 
Deposition Author(s): Prasad, R., Batra, V.K., Yang, X.-P., Krahn, J.M., Pedersen, L.C., Beard, W.A., Wilson, S.H.

Revision History 

• Version 1.0: 2007-04-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance