PDBsum entry 1ok7

Transferase

PDB id: 1ok7

Contents

Protein chains

366 a.a. *

Ligands

ARG-GLN-LEU-VAL-LEU-GLY-LEU

Waters ×460

* Residue conservation analysis

PDB id:

1ok7

Name:

Transferase

Title:

A conserved protein binding-site on bacterial sliding clamps

Structure:

DNA polymerase iii. Chain: a, b. Synonym: polymerase, dnan, b3701, c4623, z5192, ecs4636. Engineered: yes. DNA polymerase iv. Chain: c. Fragment: c-terminus of DNA pol iv residues 336-351. Synonym: pol iv. Engineered: yes.

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: dnan gene. Synthetic: yes. Organism_taxid: 562

Biol. unit:

Trimer (from PDB file)

Resolution:

1.65Å R-factor: 0.203 R-free: 0.229

Authors:

D.Y.Burnouf,V.Olieric,J.Wagner,S.Fujii,J.Reinbolt,R.P.P.Fuchs,P.Dumas

Key ref:

D.Y.Burnouf et al. (2004). Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases. J Mol Biol, 335, 1187-1197. PubMed id: 14729336 DOI: 10.1016/j.jmb.2003.11.049

Date:

18-Jul-03 Release date: 15-Jul-04

Protein chains

P0A988  (DPO3B_ECOLI) -  Beta sliding clamp from Escherichia coli (strain K12)

Seq: 366 a.a.

Struc: 366 a.a.

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

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

Added reference

DOI no: 10.1016/j.jmb.2003.11.049

J Mol Biol 335:1187-1197 (2004)

PubMed id: 14729336

Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases.

D.Y.Burnouf, V.Olieric, J.Wagner, S.Fujii, J.Reinbolt, R.P.Fuchs, P.Dumas.

ABSTRACT

Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the beta sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16). The seven C-terminal residues bind to a pocket located at the surface of one beta monomer. This region was previously identified as the binding site of another beta clamp binding protein, the delta subunit of the gamma complex. We show that peptide P16 competitively prevents beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase activities, suggesting that the site of interaction of the alpha subunit with beta is identical with, or overlaps that of Pol IV. This common binding site for delta, Pol IV and alpha subunit is shown to be formed by residues that are highly conserved among many bacterial beta homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design.

Selected figure(s)

Figure 1.
Figure 1. A, Ribbon representation of the b-ring with one bound P16 peptide. Only the seven C-terminal residues of the peptide were structured and modelled into the density map (coloured in yellow). B, Fourier difference maps around the visible part of P16 with (F[o] -F[c]) coefficients in red, and with (2F[o] -F[c]) coefficients in blue.

Figure 3.
Figure 3. A, Sequence alignment of the d subunit of g complex and of DNA polymerase IV b-binding peptides with the corresponding consensus sequence.[12.] The most conserved residues are highlighted in blue and the red lines delimit sub-sites 1 and 2 (see Results and Discussion). B, Schematic representation of the b-binding pocket. Peptide P16 is drawn in red, highly conserved b residues are boxed in green and less conserved residues in open boxes. Green, black and open circles identify b residues interacting with the most conserved residues of peptide P16, i.e. residues L16, L14 and Q11, respectively. Green and white bars on the right identify the conserved and less conserved parts within the two sub-sites, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 335, 1187-1197) copyright 2004.

Figures were selected by an automated process.