PDBsum entry 2oug

Transcription

PDB id: 2oug

Contents

Protein chains

141 a.a. *

Waters ×477

* Residue conservation analysis

PDB id:

2oug

Name:

Transcription

Title:

Crystal structure of the rfah transcription factor at 2.1a resolution

Structure:

Transcriptional activator rfah. Chain: a, b, c, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: rfah, hlyt, sfrb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.238 R-free: 0.273

Authors:

D.G.Vassylyev,M.N.Vassylyeva,V.Svetlov,I.Artsimovitch

Key ref:

G.A.Belogurov et al. (2007). Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol Cell, 26, 117-129. PubMed id: 17434131 DOI: 10.1016/j.molcel.2007.02.021

Date:

10-Feb-07 Release date: 01-May-07

Protein chains

P0AFW0  (RFAH_ECOLI) -  Transcription antitermination protein RfaH from Escherichia coli (strain K12)

Seq: 162 a.a.

Struc: 141 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.molcel.2007.02.021

Mol Cell 26:117-129 (2007)

PubMed id: 17434131

Structural basis for converting a general transcription factor into an operon-specific virulence regulator.

G.A.Belogurov, M.N.Vassylyeva, V.Svetlov, S.Klyuyev, N.V.Grishin, D.G.Vassylyev, I.Artsimovitch.

ABSTRACT

RfaH, a paralog of the general transcription factor NusG, is recruited to elongating RNA polymerase at specific regulatory sites. The X-ray structure of Escherichia coli RfaH reported here reveals two domains. The N-terminal domain displays high similarity to that of NusG. In contrast, the alpha-helical coiled-coil C domain, while retaining sequence similarity, is strikingly different from the beta barrel of NusG. To our knowledge, such an all-beta to all-alpha transition of the entire domain is the most extreme example of protein fold evolution known to date. Both N domains possess a vast hydrophobic cavity that is buried by the C domain in RfaH but is exposed in NusG. We propose that this cavity constitutes the RNA polymerase-binding site, which becomes unmasked in RfaH only upon sequence-specific binding to the nontemplate DNA strand that triggers domain dissociation. Finally, we argue that RfaH binds to the beta' subunit coiled coil, the major target site for the initiation sigma factors.

Selected figure(s)

Figure 1.
Figure 1. Structure of the RfaH Protein
(A) The overall structure.
(B) Stereo view of the RfaH interdomain interface. All structural figures were prepared using the programs MOLSCRIPT, BOBSCRIPT, and Raster3D (Esnouf, 1999, Kraulis, 1991 and Merrit and Bacon, 1997).

Figure 6.
Figure 6. The Model of RfaH Recruited to the TEC
(A) Overall model is presented in two distinct orientations. The RNAP is shown in gray with the β′CC (the RfaH-binding site) highlighted in magenta. The color scheme for the RfaH N and C domains is the same as in Figure 1. The RNAP active site is marked by the Mg^2+ ion (magenta sphere). The template DNA, the nontemplate DNA, and the RNA transcript are colored in red, green, and yellow, respectively.
(B) The close-up stereo view of RfaH bound to the β′CC. The side chains forming the intermolecular hydrophobic core are represented by the balls-and-sticks model (blue and magenta for the RfaH and β′CC, respectively). The nontemplate strand nucleotides adjacent to RfaH in the TEC model are shown in green and are numbered with respect to the position of the acceptor template base (register n). The cluster of the RfaH residues that confer defects in the ops DNA binding is colored in red.
(C) Transcript elongation on pIA349 template (Figure 4C) by RNAPs containing I290R or I291R substitutions at the tip of the β′CC in the absence (left panels) or in the presence (right panels) of full-length RfaH. Quantification is presented in Figure S6.

The above figures are reprinted by permission from Cell Press: Mol Cell (2007, 26, 117-129) copyright 2007.

Figures were selected by an automated process.