Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21359.98 
• Atom Count: 1416 
• Residue Count: 186 
• Unique protein chains: 1

1J54

Structure of the N-terminal exonuclease domain of the epsilon subunit of E.coli DNA polymerase III at pH 5.8

• DOI: 10.2210/pdb1J54/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Enterobacteria phage T7


• Deposited: 2002-01-22 Released: 2002-10-16 
• Deposition Author(s): Hamdan, S., Carr, P.D., Brown, S.E., Ollis, D.L., Dixon, N.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.234 
• R-Value Work: 0.201 

Literature

Structural Basis for Proofreading during Replication of the Escherichia coli Chromosome

Hamdan, S., Carr, P.D., Brown, S.E., Ollis, D.L., Dixon, N.E.

(2002) Structure 10: 535-546

• PubMed: 11937058 
• Primary Citation of Related Structures:  
  1J53


• PubMed Abstract: 
  

The epsilon subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3'-5' exonuclease. Structures of its catalytic N-terminal domain (epsilon186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7-1.8 A, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5'-monophosphate. The protein structure is built around a core five-stranded beta sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for epsilon and to produce a plausible model of the complex of epsilon186 with DNA.

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Organizational Affiliation: 

Research School of Chemistry, Australian National University, Canberra, ACT, Australia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase III, epsilon chain	A	186	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: dnaQ (mutD) EC: 2.7.7.7
Find proteins for P03007 (Escherichia coli (strain K12)) Go to UniProtKB:  P03007

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
TMP	A	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.234 
• R-Value Work: 0.201 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 60.800	α = 90.00
b = 60.800	β = 90.00
c = 111.100	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CCP4	model building
CNS	refinement
CCP4	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-22 
• Released Date: 2002-10-16 
• Deposition Author(s): Hamdan, S., Carr, P.D., Brown, S.E., Ollis, D.L., Dixon, N.E.

Revision History 

• Version 1.0: 2002-10-16
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance