4GX9

Crystal structure of a DNA polymerase III alpha-epsilon chimera

Summary for 4GX9

• Entry DOI: 10.2210/pdb4gx9/pdb
• Related: 1J53 1J54 2GUI 2HNH 2HQA 2IDO 4GX8
• Descriptor: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha (2 entities in total)
• Functional Keywords: dna polymerase iii, poliii epsilon, poliii alpha, dnaq, dnae, transferase
• Biological source: Escherichia coli; More
• Cellular location: Cytoplasm: P10443
• Total number of polymer chains: 4
• Total formula weight: 142786.05

Authors

Li, N.,Horan, N.,Xu, Z.-Q.,Jacques, D.,Dixon, N.E.,Oakley, A.J. (deposition date: 2012-09-04, release date: 2013-04-03, Last modification date: 2023-11-08)

Primary citation

Ozawa, K.,Horan, N.P.,Robinson, A.,Yagi, H.,Hill, F.R.,Jergic, S.,Xu, Z.Q.,Loscha, K.V.,Li, N.,Tehei, M.,Oakley, A.J.,Otting, G.,Huber, T.,Dixon, N.E.
Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits alpha, {varepsilon}, theta and beta reveals a highly flexible arrangement of the proofreading domain
Nucleic Acids Res., 41:5354-5367, 2013

PubMed Abstract: A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. Nuclear magnetic resonance experiments with reconstituted αεθ:β2 demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of ε with its α-binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p-benzoyl-L-phenylalanine incorporated at different sites in the α-PHP domain confirm the conformational variability of the tether. Structural models of the αεθ:β2 replicase complex with primer-template DNA combine all available structural data.

PubMed: 23580545
DOI: 10.1093/nar/gkt162

Experimental method

X-RAY DIFFRACTION (2.15 Å)