1J53 | pdb_00001j53

Structure of the N-terminal Exonuclease Domain of the Epsilon Subunit of E.coli DNA Polymerase III at pH 8.5

• PDB DOI: https://doi.org/10.2210/pdb1J53/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia phage T7
• Mutation(s): No 


• 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: 1.80 Å
• R-Value Free: 
  0.227 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.216 (DCC) 

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 
• DOI: https://doi.org/10.1016/s0969-2126(02)00738-4
• Primary Citation Related Structures: 
  1J53, 1J54


• 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.62 kDa 
• Atom Count: 1,641 
• Modeled Residue Count: 174 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TMP	D [auth A], E [auth A]	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N
EDO	F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.227 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.216 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.8	α = 90
b = 60.8	β = 90
c = 111.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary