PDBsum entry 5nss

Transcription

PDB id: 5nss

Contents

Protein chains

238 a.a.

1340 a.a.

1352 a.a.

74 a.a.

(+ 0 more) 248 a.a.

388 a.a.

DNA/RNA

PDB id:

5nss

Name:

Transcription

Title:

Cryo-em structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator pspf intermedate 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 k-12. Organism_taxid: 83333. Gene: rpoa, pez, phs, sez, b3295, jw3257. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: gold plyss ag. Gene: rpob, gron, nitb, rif, ron, stl, stv, tabd, b3987, jw3950. Gene: rpoc, tabb, b3988, jw3951. Gene: rpoz, b3649, jw3624.

Authors:

R.Glyde,F.Z.Ye,V.C.Darbari,N.Zhang,M.Buck,X.D.Zhang

Key ref:

R.Glyde et al. (2017). Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol Cell, 67, 106. PubMed id: 28579332

Date:

26-Apr-17 Release date: 28-Jun-17

Protein chains

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

Seq: 329 a.a.

Struc: 238 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: 1352 a.a.*

Protein chain

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

Seq: 91 a.a.

Struc: 74 a.a.

Protein chains

P37344  (PSPF_ECOLI) -  Psp operon transcriptional activator from Escherichia coli (strain K12)

Seq: 325 a.a.

Struc: 248 a.a.

Protein chain

P06223  (RP54_KLEOX) -  RNA polymerase sigma-54 factor from Klebsiella oxytoca

Seq: 477 a.a.

Struc: 388 a.a.*

* PDB and UniProt seqs differ at 156 residue positions (black crosses)

DNA/RNA chains

C-A-G-G-G-C-T-G-A-T-C-G-T-G-C-A-A-A-A-G-T-C-G-T-G-C-C-A-G-C-C-G-T-C-T 35 bases

A-G-A-C-G-G-C-T-G-G-C-A-C-G-A-C-T-T-T-T-G-C-C-A-A-G-C-C-C-T-G 31 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

Mol Cell 67:106 (2017)

PubMed id: 28579332

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

R.Glyde, F.Ye, V.C.Darbari, N.Zhang, M.Buck, X.Zhang.

ABSTRACT

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ⁵⁴factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ⁵⁴interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ⁵⁴that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.