PDBsum entry 1b4b

Repressor

PDB id: 1b4b

Contents

Protein chains

71 a.a. *

Ligands

ARG ×3

Waters ×200

* Residue conservation analysis

PDB id:

1b4b

Name:

Repressor

Title:

Structure of the oligomerization domain of the arginine repressor from bacillus stearothermophilus

Structure:

Arginine repressor. Chain: a, b, c. Fragment: oligomerization domain, l-arginine binding domain

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.20Å R-factor: 0.218 R-free: 0.266

Authors:

J.Ni,V.Sakanyan,D.Charlier,N.Glansdorff,G.D.Van Duyne

Key ref:

J.Ni et al. (1999). Structure of the arginine repressor from Bacillus stearothermophilus. Nat Struct Biol, 6, 427-432. PubMed id: 10331868 DOI: 10.1038/8229

Date:

18-Dec-98 Release date: 15-Jun-99

Protein chains

O31408  (ARGR_GEOSE) -  Arginine repressor from Geobacillus stearothermophilus

Seq: 149 a.a.

Struc: 71 a.a.

DOI no: 10.1038/8229

Nat Struct Biol 6:427-432 (1999)

PubMed id: 10331868

Structure of the arginine repressor from Bacillus stearothermophilus.

J.Ni, V.Sakanyan, D.Charlier, N.Glansdorff, G.D.Van Duyne.

ABSTRACT

The arginine repressor (ArgR) is a hexameric DNA-binding protein that plays a multifunctional role in the bacterial cell. Here, we present the 2.5 A structure of apo-ArgR from Bacillus stearothermophilus and the 2.2 A structure of the hexameric ArgR oligomerization domain with bound arginine. This first view of intact ArgR reveals an approximately 32-symmetric hexamer of identical subunits, with six DNA-binding domains surrounding a central oligomeric core. The difference in quaternary organization of subunits in the arginine-bound and apo forms provides a possible explanation for poor operator binding by apo-ArgR and for high affinity binding in the presence of arginine.

Selected figure(s)

Figure 2.
Figure 2. a, Ribbon drawing of the ArgRBst-C hexamer, viewed along the local threefold symmetry axis. Bound arginine molecules are drawn as ball-and-stick models. b, Ribbon drawing of the ArgRBst-C hexamer with bound arginines, viewed along a dyad symmetry axis, perpendicular to the view in (a). c, Superposition of C atoms for the apo-ArgRBst core hexamer (pink and green trimers) and the ArgRBst-C core hexamer (blue). Only the bottom (pink) trimer of the ArgRBst core hexamer was used to perform the superposition (r.m.s. difference of 1 Å). The view is the same as in (a). d, Superposition as in (c), except viewed along a dyad axis, as in ( b). Figs 2, 3a,b, and 4 were prepared using RIBBONS^33.

Figure 4.
Figure 4. a, Model of the apo-ArgRBst−DNA interaction. The apoArgRBst hexamer is shown superimposed on the arginine-bound ArgRBst−C hexamer as in Fig. 2c, but with the bottom trimers removed for clarity. DNA-binding domains are labeled a-f at the 3 helices. The bent DNA duplex from the CAP/DNA complex^23 was extended in both directions to give a total length of 38 base pairs, docked with the apo-ArgRBst hexamer, then undocked for clarity. Arrows indicate clashes between the 3 helices and the phosphate backbone of the DNA duplex. b, Model of the arginine-bound ArgRBst−DNA interaction. The top (green) trimer in ArgRBst was independently rotated (by ~15°) onto the ArgRBst-C core trimer to approximate the quaternary structure of ArgRBst in the arginine-bound state. Arrows indicate 3-major groove contacts when docked with the hexamer in the orientation shown. c, Schematic representation of ArgR DNA operators. E. coli operators contain 18 base pair 'Arg boxes' separated by a 2−3 base pair spacer^21, ^22. Arrows indicate 9 base pair half-sites that are arranged as inverted repeats within the E. coli consensus Arg box sequence. The B. subtilis and B. stearothermophilus operator sequences show only limited homology to the E. coli operators, but similar nuclease and chemical protection patterns and the ability of B. subtilis AhrC to complement ArgR functions in E. coli indicate that the repressor−operator interactions are closely related^3, ^8.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 427-432) copyright 1999.

Figures were selected by an automated process.