Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 28.39 kDa 
• Atom Count: 2081 
• Residue Count: 240 
• Unique protein chains: 1

2VAN

Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses

• DOI: 10.2210/pdb2VAN/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-09-03 Released: 2008-04-15 
• Deposition Author(s): Chan, H., Chou, C., Tang, K., Niebuhr, M., Tung, C., Tsai, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Mismatched Dntp Incorporation by DNA Polymerase Beta Does not Proceed Via Globally Different Conformational Pathways.

Tang, K., Niebuhr, M., Tung, C., Chan, H., Chou, C., Tsai, M.

(2008) Nucleic Acids Res 36: 2948

• PubMed: 18385153 
• DOI: 10.1093/nar/gkn138
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Understanding how DNA polymerases control fidelity requires elucidation of the mechanisms of matched and mismatched dNTP incorporations. Little is known about the latter because mismatched complexes do not crystallize readily. In this report, we employed small-angle X-ray scattering (SAXS) and structural modeling to probe the conformations of different intermediate states of mammalian DNA polymerase beta (Pol beta) in its wild-type and an error-prone variant, I260Q. Our structural results indicate that the mismatched ternary complex lies in-between the open and the closed forms, but more closely resembles the open form for WT and the closed form for I260Q. On the basis of molecular modeling, this over-stabilization of mismatched ternary complex of I260Q is likely caused by formation of a hydrogen bonding network between the side chains of Gln(260), Tyr(296), Glu(295) and Arg(258), freeing up Asp(192) to coordinate MgdNTP. These results argue against recent reports suggesting that mismatched dNTP incorporations follow a conformational path distinctly different from that of matched dNTP incorporation, or that its conformational closing is a major contributor to fidelity.

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Organizational Affiliation: 

Departments of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA POLYMERSE BETA	A	245	Rattus norvegicus	Mutation(s): 1  Gene Names: Polb EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for P06766 (Rattus norvegicus) Go to UniProtKB:  P06766

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.862	α = 90
b = 119.43	β = 90
c = 38.013	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-09-03 
• Released Date: 2008-04-15 
Deposition Author(s): Chan, H., Chou, C., Tang, K., Niebuhr, M., Tung, C., Tsai, M.

Revision History 

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance