PDBsum entry 6m6c

Transcription

PDB id: 6m6c

Contents

Protein chains

226 a.a.

1111 a.a.

1305 a.a.

94 a.a.

DNA/RNA

Metals

_MG

_ZN ×2

PDB id:

6m6c

Name:

Transcription

Title:

Cryoem structure of thermus thermophilus RNA polymerase elongation complex

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta. DNA-directed RNA polymerase subunit beta'.

Source:

Thermus thermophilus (strain hb8 / atcc 27634 / dsm 579). Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Synthetic: yes. Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274

Authors:

J.Shi,A.Wen,Y.Feng

Key ref:

J.Shi et al. (2020). Structural basis of Mfd-dependent transcription termination. Nucleic Acids Res, 48, 11762-11772. PubMed id: 33068413 DOI: 10.1093/nar/gkaa904

Date:

14-Mar-20 Release date: 14-Oct-20

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: 226 a.a.

Protein chain

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

Seq: 1119 a.a.

Struc: 1111 a.a.

Protein chain

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

Seq: 1524 a.a.

Struc: 1305 a.a.

Protein chain

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

Seq: 99 a.a.

Struc: 94 a.a.

DNA/RNA chains

C-G-G-A-G-A-G-G-U-A 10 bases

G-G-G-C-T-A-G-A-C-G-G-C-G-A-A-T-A-C-C-C 20 bases

G-G-G-T-A-T-T-C-G-C-C-G-T-G-T-A-C-C-T-C-T-C-C-T-A-G-C-C-C 29 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E: 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: 10.1093/nar/gkaa904

Nucleic Acids Res 48:11762-11772 (2020)

PubMed id: 33068413

Structural basis of Mfd-dependent transcription termination.

J.Shi, A.Wen, M.Zhao, S.Jin, L.You, Y.Shi, S.Dong, X.Hua, Y.Zhang, Y.Feng.

ABSTRACT

Mfd-dependent transcription termination plays an important role in transcription-coupled DNA repair, transcription-replication conflict resolution, and antimicrobial resistance development. Despite extensive studies, the molecular mechanism of Mfd-dependent transcription termination in bacteria remains unclear, with several long-standing puzzles. How Mfd is activated by stalled RNA polymerase (RNAP) and how activated Mfd translocates along the DNA are unknown. Here, we report the single-particle cryo-electron microscopy structures of T. thermophilus Mfd-RNAP complex with and without ATPγS. The structures reveal that Mfd undergoes profound conformational changes upon activation, contacts the RNAP β1 domain and its clamp, and pries open the RNAP clamp. These structures provide a foundation for future studies aimed at dissecting the precise mechanism of Mfd-dependent transcription termination and pave the way for rational drug design targeting Mfd for the purpose of tackling the antimicrobial resistance crisis.