3F2B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of PolC reveals unique DNA binding and fidelity determinants.

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.

(2008) Proc.Natl.Acad.Sci.USA 105: 20695-20700

  • DOI: 10.1073/pnas.0809989106
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

    Replidyne, Inc., Louisville, CO 80027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed DNA polymerase III alpha chain
A
1041Geobacillus kaustophilus (strain HTA426)Mutation(s): 0 
Gene Names: polC
EC: 2.7.7.7
Find proteins for Q5L0J3 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L0J3
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3'P17N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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'T22N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DGT
Query on DGT

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Download CCD File 
A
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 116.174α = 90.00
b = 140.793β = 90.00
c = 184.524γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy