PDBsum entry 2eul

Transcription

PDB id: 2eul

Contents

Protein chains

156 a.a. *

Metals

_ZN ×25

Waters ×386

* Residue conservation analysis

PDB id:

2eul

Name:

Transcription

Title:

Structure of the transcription factor gfh1.

Structure:

Anti-cleavage anti-grea transcription factor gfh1. Chain: a, b, c, d. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: gfhi. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Not given

Resolution:

2.40Å R-factor: 0.206 R-free: 0.245

Authors:

J.Symersky,A.Perederina,M.N.Vassylyeva,V.Svetlov,I.Artsimovitch, D.G.Vassylyev,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

J.Symersky et al. (2006). Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors. J Biol Chem, 281, 1309-1312. PubMed id: 16298991 DOI: 10.1074/jbc.C500405200

Date:

28-Oct-05 Release date: 15-Nov-05

Protein chains

Q5SJG6  (GFH1_THET8) -  Transcription inhibitor protein Gfh1 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 156 a.a.

Struc: 156 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.C500405200

J Biol Chem 281:1309-1312 (2006)

PubMed id: 16298991

Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors.

J.Symersky, A.Perederina, M.N.Vassylyeva, V.Svetlov, I.Artsimovitch, D.G.Vassylyev.

ABSTRACT

Gre factors enhance the intrinsic endonucleolytic activity of RNA polymerase to rescue arrested transcription complexes and are thought to confer the high fidelity and processivity of RNA synthesis. The Gre factors insert the extended alpha-helical coiled-coil domains into the RNA polymerase secondary channel to position two invariant acidic residues at the coiled-coil tip near the active site to stabilize the catalytic metal ion. Gfh1, a GreA homolog from Thermus thermophilus, inhibits rather than activates RNA cleavage. Here we report the structure of the T. thermophilus Gfh1 at 2.4 A resolution revealing a two-domain architecture closely resembling that of GreA. However, the interdomain orientation is strikingly distinct (approximately 162 degrees rotation) between the two proteins. In contrast to GreA, which has two acidic residues on a well fixed self-stabilized alpha-turn, the tip of the Gfh1 coiled-coil is flexible and contains four acidic residues. This difference is likely the key to the Gre functional diversity, while Gfh1 inhibits exo- and endonucleolytic cleavage, RNA synthesis, and pyrophosphorolysis, GreA enhances only the endonucleolytic cleavage. We propose that Gfh1 acidic residues stabilize the RNA polymerase active center in a catalytically inactive configuration through Mg2+-mediated interactions. The excess of the acidic residues and inherent flexibility of the coiled-coil tip might allow Gfh1 to adjust its activity to structurally distinct substrates, thereby inhibiting diverse catalytic reactions of RNA polymerase.

Selected figure(s)

Figure 1.
The Gfh1 structure and comparison with GreA and DksA. A, alignment of the Gfh1 and GreA sequences. The residues with conserved chemical properties among Gfh1 and GreA sequences that might thus form the Gfh1-like (hydrophobic) and GreA-like (”polar“) interface in both protein families are marked with yellow and green boxes, respectively, whereas the unfavorable substitutions in both Gfh1 and GreA are outlined by red boxes. The potentially functionally crucial segments at the tip of the CC-domains are highlighted with magenta. B, the structure of the Gfh1 protein. The acidic side chains at the CC tip are shown in red. C, the Gfh1 and GreA structures superimposed by the G-domains. D, the CC tips of DksA (green), GreA (yellow), and Gfh1 (cyan). DksA and GreA are superimposed by the CC-domains, and the Gfh1 CC tip is shown in a similar orientation. The hydrogen bonds stabilizing the α-turns in GreA, and DksA are shown as white dashed lines.

Figure 3.
Proposed mechanisms of the Gfh1 action. A and B, the flexibility and the number of the acidic residues at the CC tip of Gfh1 allow for the alternative binding (MG1 or MG2) of the Mg^2+ ions. C, two hypothetical pathways (competitive and noncompetitive) by which the Gfh1 protein may inhibit nucleotide addition. cMg1 and cMg2 are the two catalytic metals, whereas iMg is a putative inhibitory Mg^2+ ion.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2006, 281, 1309-1312) copyright 2006.

Figures were selected by an automated process.