PDBsum entry 3dxj

Transcription,transferase

PDB id: 3dxj

Contents

Protein chains

231 a.a. *

243 a.a. *

1119 a.a. *

1504 a.a. *

95 a.a. *

349 a.a. *

Ligands

PO4 ×2

MPD ×3

NE6 ×2

Metals

_MG ×3

_ZN ×4

Waters ×30

* Residue conservation analysis

PDB id:

3dxj

Name:

Transcription,transferase

Title:

Crystal structure of thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic myxopyronin

Structure:

DNA-directed RNA polymerase subunit alpha. Chain a, b, k, l. Chain: a, b, k, l. Bacterial RNA polymerase beta subunit. Chain c, m. Chain: c, m. Bacterial RNA polymerase beta-prime subunit. Chain d, n. Chain: d, n. Bacterial RNA polymerase omega subunit. Chain e, o. Chain: e, o.

Source:

Thermus thermophilus hb8. Organism_taxid: 300852. Organism_taxid: 300852

Resolution:

3.00Å R-factor: 0.235 R-free: 0.289

Authors:

K.Das,E.Arnold

Key ref:

J.Mukhopadhyay et al. (2008). The RNA polymerase "switch region" is a target for inhibitors. Cell, 135, 295-307. PubMed id: 18957204 DOI: 10.1016/j.cell.2008.09.033

Date:

24-Jul-08 Release date: 14-Oct-08

Protein chains

Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 315 a.a.

Struc: 231 a.a.

Protein chains

Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 315 a.a.

Struc: 243 a.a.

Protein chains

Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1119 a.a.

Struc: 1119 a.a.

Protein chains

Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta' from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1524 a.a.

Struc: 1504 a.a.

Protein chains

Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 99 a.a.

Struc: 95 a.a.*

Protein chains

Q5SKW1  (Q5SKW1_THET8) -  RNA polymerase sigma factor SigA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 423 a.a.

Struc: 349 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, K, L, M, N, O, P: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.cell.2008.09.033

Cell 135:295-307 (2008)

PubMed id: 18957204

The RNA polymerase "switch region" is a target for inhibitors.

J.Mukhopadhyay, K.Das, S.Ismail, D.Koppstein, M.Jang, B.Hudson, S.Sarafianos, S.Tuske, J.Patel, R.Jansen, H.Irschik, E.Arnold, R.H.Ebright.

ABSTRACT

The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP). Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP "switch region"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA. We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation. We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx. The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.

Selected figure(s)

Figure 1.
Figure 1. RNAP Clamp, RNAP Switch Region, and Antibiotics Studied
(A) Conformational states of the RNAP clamp (two orthogonal views). Structure of RNAP showing open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Circle, switch region; dashed circle, binding site for rifamycins; violet sphere, active-center Mg^2+.
(B) Conformational states of the RNAP switch region (stereoview). Structure of RNAP switch 1 and RNAP switch 2 (β′ residues 1304–1329 and β′ residues 330–349; residues numbered as in E. coli RNAP) showing conformational states associated with open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Gray squares, points of connection of switch 1 and switch 2 to the RNAP main mass. Colored circles, points of connection of switch 1 and switch 2 to the RNAP clamp.
(C) Structures of myxopyronin A (Myx), corallopyronin A (Cor), and ripostatin A (Rip).

Figure 4.
Figure 4. Structural Basis of Transcription Inhibition by Myx: Structure of the RNAP-Myx Complex
(A) Overall structure (two orthogonal views; β′ nonconserved region and σ omitted for clarity). View orientations are as in Figure 1A. Green, Myx; violet sphere, active-center Mg^2+.
(B) Myx binding region (stereoview). Residues are numbered both as in T. thermophilus RNAP and as in E. coli RNAP (in parentheses). Green, Myx; red, sites of single-residue substitutions that confer high-level resistance to Myx.

The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2008, 135, 295-307) copyright 2008.

Figures were selected by an automated process.