PDBsum entry 2ro4

Transcription

PDB id: 2ro4

Contents

Protein chains

53 a.a. *

* Residue conservation analysis

PDB id:

2ro4

Name:

Transcription

Title:

Rdc-refined solution structure of the n-terminal DNA recognition domain of the bacillus subtilis transition-state regulator abrb

Structure:

Transition state regulatory protein abrb. Chain: a, b. Fragment: n-terminal DNA recognition domain. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: abrb. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

10 models

Authors:

D.M.Sullivan,B.G.Bobay,D.J.Kojetin,R.J.Thompson,M.Rance,M.A.Strauch, J.Cavanagh

Key ref:

D.M.Sullivan et al. (2008). Insights into the Nature of DNA Binding of AbrB-like Transcription Factors. Structure, 16, 1702-1713. PubMed id: 19000822 DOI: 10.1016/j.str.2008.08.014

Date:

08-Mar-08 Release date: 11-Nov-08

Protein chains

P08874  (ABRB_BACSU) -  Transition state regulatory protein AbrB from Bacillus subtilis (strain 168)

Seq: 96 a.a.

Struc: 53 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.str.2008.08.014

Structure 16:1702-1713 (2008)

PubMed id: 19000822

Insights into the Nature of DNA Binding of AbrB-like Transcription Factors.

D.M.Sullivan, B.G.Bobay, D.J.Kojetin, R.J.Thompson, M.Rance, M.A.Strauch, J.Cavanagh.

ABSTRACT

Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these "transition-state regulator" proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators: AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel-shift assays, and mutagenic and NMR studies to generate a structural model of the complex between AbrBN(55) and its cognate promoter, abrB8. These investigations have enabled us to generate a model for the specific nature of the transition-state regulator-DNA interaction, a structure that has remained elusive thus far.

Selected figure(s)

Figure 2.
Figure 2. Structural Similarities and Differences among AbrBN^53, AbhN, and SpoVTN
(A–F) Critical arginine residues involved in DNA binding orientations for (A) R8; (B) R15; and (C) R23 and R24 from AbrBN^53 (red), AbhN (gold), and SpoVTN (green). Comparison of the electrostatic surface potential between (D) AbrBN^53, (E) AbhN, and (F) SpoVTN. Blue regions indicate positive charge, whereas red regions indicate negative charge. Proteins are oriented as depicted in Figure 1.

Figure 4.
Figure 4. Lowest-Energy DNA-Bound AbrBN^55 Model from Semi-Flexible Docking and Comparison to Unbound AbrBN^53
(A) Two views of the lowest-energy HADDOCK structure from the semi-flexible docking studies. Disulfide linkages are shown as spheres in the image. Insets show a detailed look at the positioning of the arginine residues involved in binding.
(B) Overlay of unbound AbrBN^53 (red) and the lowest HADDOCK score model of AbrBN^55 bound to abrB8 (blue). One monomer is highlighted for clarity.
(C) The degree of structural variation between the unbound AbrBN^53 NMR structure and the modeled AbrBN^55 bound to abrB8, colored from white (little variation) to red (large variation), as calculated in the Cα alignment by THESEUS plotted on the refined AbrBN^53 solution structure. The unbound and bound AbrBN^53 dimer structures overlay with a Cα rmsd of 2.84 Å. LP1 and LP2 (chain A) and LP1′ and LP2′ (chain B) are noted. Proteins are oriented as depicted in Figure 1 on structures most similar to the average structure in the ensemble reported by THESEUS.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1702-1713) copyright 2008.

Figures were selected by an automated process.