PDBsum entry 3f2d

Transferase/DNA

PDB id: 3f2d

Contents

Protein chain

993 a.a. *

DNA/RNA

Ligands

PO4 ×2

DGT

Metals

_MN ×3

_ZN ×2

Waters ×101

* Residue conservation analysis

PDB id:

3f2d

Name:

Transferase/DNA

Title:

DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp, mn and zn

Structure:

5'-d( Dcp Dap Dgp Dtp Dgp Dap Dgp Dap Dcp Dgp Dgp Dgp Dcp D ap Dap Dcp Dc)-3'. Chain: p. Engineered: yes. Other_details: DNA primer strand. 5'-d( Dap Dtp Dap Dap Dcp Dgp Dgp Dtp Dtp Dgp Dcp Dcp Dcp D gp Dtp Dcp Dtp Dcp Dap Dcp Dtp Dg)-3'. Chain: t. Engineered: yes.

Source:

Synthetic: yes. Other_details: primer strand is synthetic oligonucleotide. Other_details: template strand is synthetic oligonucleotide. Geobacillus kaustophilus. Organism_taxid: 1462. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.51Å R-factor: 0.218 R-free: 0.254

Authors:

D.R.Davies,R.J.Evans,J.M.Bullard,J.Christensen,L.S.Green,J.W.Guiles, W.K.Ribble,N.Janjic,T.C.Jarvis

Key ref:

R.J.Evans et al. (2008). Structure of PolC reveals unique DNA binding and fidelity determinants. Proc Natl Acad Sci U S A, 105, 20695-20700. PubMed id: 19106298 DOI: 10.1073/pnas.0809989106

Date:

29-Oct-08 Release date: 20-Jan-09

Protein chain

Q5L0J3  (Q5L0J3_GEOKA) -  DNA polymerase III PolC-type from Geobacillus kaustophilus (strain HTA426)

Seq: 1444 a.a.

Struc: 993 a.a.

DNA/RNA chains

G-A-G-A-C-G-G-G-C-A-A-C-C 13 bases

A-T-A-A-C-G-G-T-T-G-C-C-C-G-T-C-T-C 18 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1073/pnas.0809989106

Proc Natl Acad Sci U S A 105:20695-20700 (2008)

PubMed id: 19106298

Structure of PolC reveals unique DNA binding and fidelity determinants.

R.J.Evans, D.R.Davies, J.M.Bullard, J.Christensen, L.S.Green, J.W.Guiles, J.D.Pata, W.K.Ribble, N.Janjic, T.C.Jarvis.

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.

Selected figure(s)

Figure 2.
PHP β-barrel architecture. Schematic representations are shown of canonical PHP (αβ)[7]-barrel (Left) (see Fig. S3), the PolC PHP domain (Center), and the TaqDnaE PHP domain [Right, based on Protein Data Bank (PDB) ID code 2HPI]. Red circles indicate the locations of metal-chelating residues. Filled red circles indicate the locations of metal-chelating residues that are conserved between PolC and TaqDnaE, open circles indicate the locations of metal-chelating residues in PolC and TaqDnaE that are not conserved in EcoDnaE.

Figure 4.
Comparison of polymerase active sites from the β-NT and classical superfamilies. The active sites and DNA substrates are shown from PolC (colored as in Fig. 1) and TaqDnaE (white; PDB ID code 3E0D) C family polymerases (A), Polβ (PDB ID code 2FMP), an X family polymerase (B), and RB69 (PDB ID code 1IG9), a B family polymerase (C). (B and C) Palms are colored magenta, and fingers are colored blue.

Figures were selected by an automated process.