2xy8

From Proteopedia

Paramagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain of the DNA polymerase III

Structural highlights

2xy8 is a 2 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO3E_ECOLI DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease.

Publication Abstract from PubMed

In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal epsilon domain of the E. coli DNA polymerase III (epsilon186) in complex with the HOT domain. Docking from the bound form of the two partners is swiftly executed (interface RMSDs < 1 A) even with addition of very large amount of noise, while the conformational changes of the free form still present some challenges (interface RMSDs in a 3.1-3.9 A range for the ten lowest energy complexes). Finally, using exclusively PCS as experimental information, we determine the structure of epsilon186 in complex with the HOT-homologue theta subunit of the E. coli DNA polymerase III.

Protein-protein HADDocking using exclusively pseudocontact shifts.,Schmitz C, Bonvin AM J Biomol NMR. 2011 May 29. PMID:21626213^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schmitz C, Bonvin AM. Protein-protein HADDocking using exclusively pseudocontact shifts. J Biomol NMR. 2011 May 29. PMID:21626213 doi:10.1007/s10858-011-9514-4