2IDO

Structure of the E. coli Pol III epsilon-Hot proofreading complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex.

Kirby, T.W., Harvey, S., DeRose, E.F., Chalov, S., Chikova, A.K., Perrino, F.W., Schaaper, R.M., London, R.E., Pedersen, L.C.

(2006) J Biol Chem 281: 38466-38471

  • DOI: 10.1074/jbc.M606917200
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The epsilon subunit of Escherichia coli DNA polymerase III possesses 3'-exonucleolytic proofreading activity. Within the Pol III core, epsilon is tightly bound between the alpha subunit (DNA polymerase) and subunit. Here, we present the crystal struc ...

    The epsilon subunit of Escherichia coli DNA polymerase III possesses 3'-exonucleolytic proofreading activity. Within the Pol III core, epsilon is tightly bound between the alpha subunit (DNA polymerase) and subunit. Here, we present the crystal structure of epsilon in complex with HOT, the bacteriophage P1-encoded homolog of , at 2.1 A resolution. The epsilon-HOT interface is defined by two areas of contact: an interaction of the previously unstructured N terminus of HOT with an edge of the epsilon central beta-sheet as well as interactions between HOT and the catalytically important helix alpha1-loop-helix alpha2 motif of epsilon. This structure provides insight into how HOT and, by implication, may stabilize the epsilon subunit, thus promoting efficient proofreading during chromosomal replication.

    Organizational Affiliation: 

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences/NIH, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III epsilon subunit
A, C
186Escherichia coliMutation(s): 0 
Gene Names: dnaQ, mutD
EC: 2.7.7.7
Find proteins for P03007 (Escherichia coli (strain K12))
Go to UniProtKB:  P03007
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hot protein
B, D
83Escherichia virus P1Mutation(s): 0 
Gene Names: hot
Find proteins for Q71T70 (Escherichia phage P1)
Go to UniProtKB:  Q71T70
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMP
Query on TMP
Download CCD File 
A, C
THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download CCD File 
A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.289α = 90
b = 77.289β = 90
c = 212.978γ = 90
Software Package:
Software NamePurpose
CNSrefinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance