PDBsum entry 2k9m

Transcription

PDB id: 2k9m

Contents

Protein chain

130 a.a. *

* Residue conservation analysis

PDB id:

2k9m

Name:

Transcription

Title:

Structure of the core binding domain of sigma54

Structure:

RNA polymerase sigma factor rpon. Chain: a. Fragment: sequence database residues 69-198. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: rpon. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

E.Hong,D.Wemmer

Key ref:

E.Hong et al. (2009). Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point. J Mol Biol, 390, 70-82. PubMed id: 19426742 DOI: 10.1016/j.jmb.2009.04.070

Date:

19-Oct-08 Release date: 26-May-09

Protein chain

O66858  (O66858_AQUAE) -  RNA polymerase sigma factor RpoN from Aquifex aeolicus (strain VF5)

Seq: 398 a.a.

Struc: 130 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2009.04.070

J Mol Biol 390:70-82 (2009)

PubMed id: 19426742

Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point.

E.Hong, M.Doucleff, D.E.Wemmer.

ABSTRACT

Transcription initiation by bacterial sigma(54)-RNA polymerase requires a conformational change of the holopolymerase-DNA complex, driven by an enhancer-binding protein. Although structures of the core polymerase and the more common sigma(70) factor have been determined, little is known about the structure of the sigma(54) variant. We report here the structure of an Aquifex aeolicus sigma(54) domain (residues 69-198), which binds core RNA polymerase. The structure is composed of two distinct subdomains held together by a small, conserved hydrophobic interface that appears to act as a fracture point in the structure. The N-terminal, four-helical subdomain has a negative surface and conserved residues that likely contact the core polymerase, while the C-terminal, three-helical bundle has a strongly positive patch that could contact DNA. Sequence conservation indicates that these structural features are conserved and are important for the role of sigma(54) in the polymerase complex.

Selected figure(s)

Figure 1.
Fig. 1. The sequence of σ^54 is indicated by the broad line. Various regions are indicated by color: yellow, interaction with EBPs; blue, CBD; orange, interaction with DNA in the − 12 region of the promoter (for which precise domain boundaries have not been identified); red, sequence-specific recognition of the − 24 promoter region.

Figure 2.
Fig. 2. ^1H–^15N HQSC spectra for the 60–135 construct (top) and the 69–198 construct (bottom), with peaks labeled by the residue assignments. Side-chain amide resonances of Asn and Gln are indicated with horizontal lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 390, 70-82) copyright 2009.

Figures were selected by an automated process.