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: 102.05 kDa 
• Atom Count: 7621 
• Residue Count: 910 
• Unique protein chains: 1

2HNH

Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III

• DOI: 10.2210/pdb2HNH/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-12 Released: 2006-09-19 
• Deposition Author(s): Meindert, M.H., Georgescu, R.E., Lee, S., O'Donnell, M., Kuriyan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 

Literature

Crystal Structure of the Catalytic alpha Subunit of E. coli Replicative DNA Polymerase III.

Lamers, M.H., Georgescu, R.E., Lee, S.G., O'donnell, M., Kuriyan, J.

(2006) Cell 126: 881-892

• PubMed: 16959568 
• DOI: 10.1016/j.cell.2006.07.028
• Primary Citation of Related Structures:  
  2HNH, 2HQA


• PubMed Abstract: 
  

Bacterial replicative DNA polymerases such as Polymerase III (Pol III) share no sequence similarity with other polymerases. The crystal structure, determined at 2.3 A resolution, of a large fragment of Pol III (residues 1-917), reveals a unique chain fold with localized similarity in the catalytic domain to DNA polymerase beta and related nucleotidyltransferases. The structure of Pol III is strikingly different from those of members of the canonical DNA polymerase families, which include eukaryotic replicative polymerases, suggesting that the DNA replication machinery in bacteria arose independently. A structural element near the active site in Pol III that is not present in nucleotidyltransferases but which resembles an element at the active sites of some canonical DNA polymerases suggests that, at a more distant level, all DNA polymerases may share a common ancestor. The structure also suggests a model for interaction of Pol III with the sliding clamp and DNA.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III alpha subunit	A	910	Escherichia coli	Mutation(s): 0  Gene Names: dnaE, polC EC: 2.7.7.7
Find proteins for P10443 (Escherichia coli (strain K12)) Explore P10443  Go to UniProtKB:  P10443

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.584	α = 90
b = 92.6	β = 90
c = 130.235	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-12 
• Released Date: 2006-09-19 
Deposition Author(s): Meindert, M.H., Georgescu, R.E., Lee, S., O'Donnell, M., Kuriyan, J.

Revision History 

• Version 1.0: 2006-09-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance