PDBsum entry 7khc

Transcription/DNA

PDB id: 7khc

Contents

Protein chains

309 a.a.

1340 a.a.

1342 a.a.

76 a.a.

447 a.a.

DNA/RNA

Ligands

POP

1N7 ×2

Metals

_ZN ×2

_MG

PDB id:

7khc

Name:

Transcription/DNA

Title:

Escherichia coli RNA polymerase and rrnbp1 promoter closed complex

Structure:

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

Source:

Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: rpoa, pez, phs, sez, b3295, jw3257. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Gene: rpob, gron, nitb, rif, ron, stl, stv, tabd, b3987, jw3950. Gene: rpoc, tabb, b3988, jw3951. Gene: rpoz, b3649, jw3624.

Authors:

Y.Shin,M.Z.Qayyum,K.S.Murakami

Key ref:

Y.Shin et al. (2021). Structural basis of ribosomal RNA transcription regulation. Nat Commun, 12, 528. PubMed id: 33483500 DOI: 10.1038/s41467-020-20776-y

Date:

20-Oct-20 Release date: 28-Oct-20

Supersedes:

6wr6

Protein chains

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

Seq: 329 a.a.

Struc: 309 a.a.

Protein chain

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

Seq: 1342 a.a.

Struc: 1340 a.a.

Protein chain

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

Seq: 1407 a.a.

Struc: 1342 a.a.

Protein chain

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

Seq: 91 a.a.

Struc: 76 a.a.

Protein chain

P00579  (RPOD_ECOLI) -  RNA polymerase sigma factor RpoD from Escherichia coli (strain K12)

Seq: 613 a.a.

Struc: 447 a.a.

DNA/RNA chains

C-A-G-A-A-A-A-T-T-A-T-T-T-T-A-A-A-T-T-T-C-C-T-C-T-T-G-T-C-A-G-G-C-C-G-G-A-A-T- 63 bases

A-G-T-G-G-T-G-G-C-G-C-A-T-T-A-T-A-G-G-G-A-G-T-T-A-T-T-C-C-G-G-C-C-T-G-A-C-A-A- 63 bases

T-G-A-C-A-C-G-G-A-C-T-C-T-A-C-G-A-G 18 bases

C-T-C-G-T-A-G-A-G-T-C-C-G-T-G-T-C-A 18 bases

Enzyme reactions

• Enzyme class 2: 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

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = POP) corresponds exactly) + diphosphate

• Enzyme class 3: Chain F: E.C.?

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

DOI no: 10.1038/s41467-020-20776-y

Nat Commun 12:528 (2021)

PubMed id: 33483500

Structural basis of ribosomal RNA transcription regulation.

Y.Shin, M.Z.Qayyum, D.Pupov, D.Esyunina, A.Kulbachinskiy, K.S.Murakami.

ABSTRACT

Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ⁷⁰ holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ_1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ_1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.