3F2D

DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mn and Zn

Summary for 3F2D

• Entry DOI: 10.2210/pdb3f2d/pdb
• Related: 3F2B 3F2C
• Descriptor: 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3', 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3', GEOBACILLUS KAUSTOPHILUS DNA POLC, ... (8 entities in total)
• Functional Keywords: dna polymerase c, dna polymerase iii, ternary complex, protein-dna complex, replicative polymerase, gram-positive, transferase-dna complex, transferase/dna
• Biological source: Geobacillus kaustophilus; More
• Cellular location: Cytoplasm : Q5L0J3
• Total number of polymer chains: 3
• Total formula weight: 130191.00

Authors

Davies, D.R.,Evans, R.J.,Bullard, J.M.,Christensen, J.,Green, L.S.,Guiles, J.W.,Ribble, W.K.,Janjic, N.,Jarvis, T.C. (deposition date: 2008-10-29, release date: 2009-01-20, Last modification date: 2023-09-06)

Primary citation

Evans, R.J.,Davies, D.R.,Bullard, J.M.,Christensen, J.,Green, L.S.,Guiles, J.W.,Pata, J.D.,Ribble, W.K.,Janjic, N.,Jarvis, T.C.
Structure of PolC reveals unique DNA binding and fidelity determinants.
Proc.Natl.Acad.Sci.USA, 105:20695-20700, 2008

PubMed Abstract: PolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-A resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique beta-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a mechanism by which the active site can communicate with the rest of the replisome to trigger proofreading after nucleotide misincorporation, leading to an integrated model for controlling the dynamic switch between replicative and repair polymerases. This ternary complex of a cellular replicative polymerase affords insights into polymerase fidelity, evolution, and structural diversity.

PubMed: 19106298
DOI: 10.1073/pnas.0809989106

Experimental method

X-RAY DIFFRACTION (2.51 Å)