PDBsum entry 6c6t

Transcription/DNA/RNA

PDB id: 6c6t

Contents

Protein chains

221 a.a.

1319 a.a.

1335 a.a.

83 a.a.

85 a.a.

DNA/RNA

Metals

_MG

_ZN ×2

PDB id:

6c6t

Name:

Transcription/DNA/RNA

Title:

Cryoem structure of e.Coli RNA polymerase elongation complex bound with rfah

Structure:

DNA (29-mer). Chain: a. Engineered: yes. DNA (29-mer). Chain: b. Engineered: yes. RNA (5'- r( Gp Cp Ap Up Up Cp Ap Ap Ap Gp Cp Cp Gp Ap Gp Ap Gp Gp Up A)-3'). Chain: r.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: rpoa, pez, phs, sez, b3295, jw3257. Expressed in: escherichia coli. Expression_system_taxid: 562.

Authors:

J.Y.Kang,I.Artsimovitch,R.Landick,S.A.Darst

Key ref:

J.Y.Kang et al. (2018). Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators. Cell, 173, 1650. PubMed id: 29887376

Date:

19-Jan-18 Release date: 25-Jul-18

Protein chains

P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha from Escherichia coli (strain K12)

Seq: 329 a.a.

Struc: 221 a.a.

Protein chain

P0A8V2  (RPOB_ECOLI) -  DNA-directed RNA polymerase subunit beta from Escherichia coli (strain K12)

Seq: 1342 a.a.

Struc: 1319 a.a.

Protein chain

P0A8T7  (RPOC_ECOLI) -  DNA-directed RNA polymerase subunit beta' from Escherichia coli (strain K12)

Seq: 1407 a.a.

Struc: 1335 a.a.

Protein chain

P0A800  (RPOZ_ECOLI) -  DNA-directed RNA polymerase subunit omega from Escherichia coli (strain K12)

Seq: 91 a.a.

Struc: 83 a.a.

Protein chain

P0AFW0  (RFAH_ECOLI) -  Transcription antitermination protein RfaH from Escherichia coli (strain K12)

Seq: 162 a.a.

Struc: 85 a.a.

DNA/RNA chains

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

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

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

Enzyme reactions

• Enzyme class 2: Chain D: E.C.?
• Enzyme class 3: Chains G, H, I, J, K: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

Cell 173:1650 (2018)

PubMed id: 29887376

Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators.

J.Y.Kang, R.A.Mooney, Y.Nedialkov, J.Saba, T.V.Mishanina, I.Artsimovitch, R.Landick, S.A.Darst.

ABSTRACT

NusG/RfaH/Spt5 transcription elongation factors are the only transcription regulators conserved across all life. Bacterial NusG regulates RNA polymerase (RNAP) elongation complexes (ECs) across most genes, enhancing elongation by suppressing RNAP backtracking and coordinating ρ-dependent termination and translation. The NusG paralog RfaH engages the EC only at operon polarity suppressor (ops) sites and suppresses both backtrack and hairpin-stabilized pausing. We used single-particle cryoelectron microscopy (cryo-EM) to determine structures of ECs at ops with NusG or RfaH. Both factors chaperone base-pairing of the upstream duplex DNA to suppress backtracking, explaining stimulation of elongation genome-wide. The RfaH-opsEC structure reveals how RfaH confers operon specificity through specific recognition of an ops hairpin in the single-stranded nontemplate DNA and tighter binding to the EC to exclude NusG. Tight EC binding by RfaH sterically blocks the swiveled RNAP conformation necessary for hairpin-stabilized pausing. The universal conservation of NusG/RfaH/Spt5 suggests that the molecular mechanisms uncovered here are widespread.