PDBsum entry 4wqt

Transferase/transcription

PDB id: 4wqt

Contents

Protein chains

(+ 0 more) 223 a.a.

1080 a.a.

1334 a.a.

93 a.a.

154 a.a.

Metals

_MG ×3

_ZN ×3

PDB id:

4wqt

Name:

Transferase/transcription

Title:

Thermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a grea/gfh1 chimeric protein)

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b, f, g, k, l. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c, h, m. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta. DNA-directed RNA polymerase subunit beta'.

Source:

Thermus thermophilus hb8. Organism_taxid: 300852. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

4.40Å R-factor: 0.260 R-free: 0.313

Authors:

Y.Murayama,S.Sekine,S.Yokoyama

Key ref:

S.Sekine et al. (2015). The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions. Mol Cell, 57, 408-421. PubMed id: 25601758 DOI: 10.1016/j.molcel.2014.12.014

Date:

22-Oct-14 Release date: 18-Feb-15

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: 223 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: 1080 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: 1334 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: 93 a.a.

Protein chains

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

Seq: 156 a.a.

Struc: 154 a.a.*

Protein chains

Q5SKM1  (Q5SKM1_THET8) -  Transcription elongation factor GreA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 155 a.a.

Struc: 154 a.a.*

* PDB and UniProt seqs differ at 92 residue positions (black crosses)

Enzyme reactions

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

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

Added reference

DOI no: 10.1016/j.molcel.2014.12.014

Mol Cell 57:408-421 (2015)

PubMed id: 25601758

The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions.

S.Sekine, Y.Murayama, V.Svetlov, E.Nudler, S.Yokoyama.

ABSTRACT

DNA-dependent RNA polymerase (RNAP) accomplishes multiple tasks during transcription by assuming different structural forms. Reportedly, the "tight" form performs nucleotide addition to nascent RNA, while the "ratcheted" form is adopted for transcription inhibition. In this study, we performed Cys-pair crosslinking (CPX) analyses of various transcription complexes of a bacterial RNAP and crystallographic analyses of its backtracked and Gre-factor-bound states to clarify which of the two forms is adopted. The ratcheted form was revealed to support GreA-dependent transcript cleavage, long backtracking, hairpin-dependent pausing, and termination. In contrast, the tight form correlated with nucleotide addition, mismatch-dependent pausing, one-nucleotide backtracking, and factor-independent transcript cleavage. RNAP in the paused/backtracked state, but not the nucleotide-addition state, readily transitions to the ratcheted form ("ratchetable"), indicating that the tight form represents two distinct regulatory states. The 3' end and the hairpin structure of the nascent RNA promote the ratchetable nature by modulating the trigger-loop conformation.