Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.86 kDa 
• Atom Count: 621 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

2AXD

solution structure of the theta subunit of escherichia coli DNA polymerase III in complex with the epsilon subunit

• PDB DOI: 10.2210/pdb2AXD/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-05 Released: 2006-07-04 
• Deposition Author(s): Keniry, M.A., Park, A.Y., Owen, E.A., Hamdan, S.M., Pintacuda, G., Otting, G., Dixon, N.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 12 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit

Keniry, M.A., Park, A.Y., Owen, E.A., Hamdan, S.M., Pintacuda, G., Otting, G., Dixon, N.E.

(2006) J Bacteriol 188: 4464-4473

• PubMed: 16740953 
• DOI: 10.1128/JB.01992-05
• Primary Citation of Related Structures:  
  2AXD


• PubMed Abstract: 
  

The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the alpha, epsilon, and theta subunits. The theta subunit is the smallest and least understood subunit. The three-dimensional structure of theta in a complex with the unlabeled N-terminal domain of the epsilon subunit, epsilon186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy3+, Er3+, or Ho3+) at the active site of epsilon186. The structure determination revealed a three-helix bundle fold that is similar to the solution structures of theta in a methanol-water buffer and of the bacteriophage P1 homolog, HOT, in aqueous buffer. Conserved nuclear Overhauser enhancement (NOE) patterns obtained for free and complexed theta show that most of the structure changes little upon complex formation. Discrepancies with respect to a previously published structure of free theta (Keniry et al., Protein Sci. 9:721-733, 2000) were attributed to errors in the latter structure. The present structure satisfies the pseudocontact shifts better than either the structure of theta in methanol-water buffer or the structure of HOT. satisfies these shifts. The epitope of epsilon186 on theta was mapped by NOE difference spectroscopy and was found to involve helix 1 and the C-terminal part of helix 3. The pseudocontact shifts indicated that the helices of theta are located about 15 A or farther from the lanthanide ion in the active site of epsilon186, in agreement with the extensive biochemical data for the theta-epsilon system.

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Organizational Affiliation: 

Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III, theta subunit	A [auth S]	76	Escherichia coli	Mutation(s): 0  Gene Names: holE EC: 2.7.7.7
UniProt
Find proteins for P0ABS8 (Escherichia coli (strain K12)) Explore P0ABS8  Go to UniProtKB:  P0ABS8

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 12 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2AXD Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-05 
• Released Date: 2006-07-04 
Deposition Author(s): Keniry, M.A., Park, A.Y., Owen, E.A., Hamdan, S.M., Pintacuda, G., Otting, G., Dixon, N.E.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations