PDBsum entry 1tty

Transcription

PDB id: 1tty

Contents

Protein chain

87 a.a. *

* Residue conservation analysis

PDB id:

1tty

Name:

Transcription

Title:

Solution structure of sigma a region 4 from thermotoga maritima

Structure:

RNA polymerase sigma factor rpod. Chain: a. Synonym: sigma-a. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: rpod, siga, tm1451. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

22 models

Authors:

L.J.Lambert,Y.Wei,V.Schirf,B.Demeler,M.H.Werner

Key ref:

L.J.Lambert et al. (2004). T4 AsiA blocks DNA recognition by remodeling sigma70 region 4. EMBO J, 23, 2952-2962. PubMed id: 15257291 DOI: 10.1038/sj.emboj.7600312

Date:

23-Jun-04 Release date: 23-Nov-04

Protein chain

P77994  (SIGA_THEMA) -  RNA polymerase sigma factor SigA from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 399 a.a.

Struc: 87 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/sj.emboj.7600312

EMBO J 23:2952-2962 (2004)

PubMed id: 15257291

T4 AsiA blocks DNA recognition by remodeling sigma70 region 4.

L.J.Lambert, Y.Wei, V.Schirf, B.Demeler, M.H.Werner.

ABSTRACT

Bacteriophage T4 AsiA is a versatile transcription factor capable of inhibiting host gene expression as an 'anti-sigma' factor while simultaneously promoting gene-specific expression of T4 middle genes in conjunction with T4 MotA. To accomplish this task, AsiA engages conserved region 4 of Eschericia coli sigma70, blocking recognition of most host promoters by sequestering the DNA-binding surface at the AsiA/sigma70 interface. The three-dimensional structure of an AsiA/region 4 complex reveals that the C-terminal alpha helix of region 4 is unstructured, while four other helices adopt a completely different conformation relative to the canonical structure of unbound region 4. That AsiA induces, rather than merely stabilizes, this rearrangement can be realized by comparison to the homologous structures of region 4 solved in a variety of contexts, including the structure of Thermotoga maritima sigmaA region 4 described herein. AsiA simultaneously occupies the surface of region 4 that ordinarily contacts core RNA polymerase (RNAP), suggesting that an AsiA-bound sigma70 may also undergo conformational changes in the context of the RNAP holoenzyme.

Selected figure(s)

Figure 2.
Figure 2 Three-dimensional structure of T. maritima A SR4. (A) Superposition of the NMR structure family. Chemical shifts for residues 379 -383 (the loop between S4 and S5) were not identified and this segment is relatively disordered in the family. (B) Helix arrangement in TmSR4. Helix S1 (residues 322 -329), helix S2 (residues 334 -342), helix S3 (residues 353 -361), helix S4 (residues 364 -377) and helix S5 (residues 385 -393) were identified from secondary 13C[ / ]shifts, d[NN] (i, i+1) NOEs and 3J[NH ]coupling constants. (C) Hydrophobic core of TmSR4 formed from nonpolar residues found in all the five helices. (D) Superposition of TmSR4 (blue), the T. aquaticus A SR4 in its DNA-bound conformation (red) (Campbell et al, 2002) and the T. thermophilus A SR4 in its holoenzyme conformation (green) (Vassylyev et al, 2002).

Figure 6.
Figure 6 AsiA remodels the conformation of SR4. The structure of TmSR4 (blue) is compared to the structure of AsiA-bound EcSR4 (green) in two views. The C-termini of helices S1 -S4 are colored red. Helix S5 seen in TmSR4 is unfolded in EcSR4 and the unfolded segment has been excluded from the views of EcSR4 for clarity. (A) Lateral view along helix S4 and (B) top view rotated 90° about the horizontal axis relative to (A). Apparent in both views, helix S2 in the complex is inverted N-to-C-terminus and helix S1 is repositioned by approximately 180° in the AsiA-bound conformation relative to the conformation in TmSR4. The DNA-binding HTH element (helices S3 and S4) is unfolded from its canonical orientation in TmSR4 and forms a pseudo-continuous helix in the AsiA-bound state.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2952-2962) copyright 2004.

Figures were selected by the author.