PDBsum entry 6psr

Transcription/DNA

PDB id: 6psr

Contents

Protein chains

230 a.a.

219 a.a.

1340 a.a.

1345 a.a.

75 a.a.

548 a.a.

73 a.a.

72 a.a.

DNA/RNA

Ligands

1N7 ×4

Metals

_ZN ×3

_MG

PDB id:

6psr

Name:

Transcription/DNA

Title:

Escherichia coli RNA polymerase promoter unwinding intermediate (trpi1) with trar and rpst p2 promoter

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: g, h, m. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. Engineered: yes. DNA-directed RNA polymerase subunit beta. Chain: i. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta.

Source:

Escherichia coli. Organism_taxid: 562. Gene: rpoa, pez, phs, sez, b3295, jw3257. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rpob, z5560, ecs4910. Gene: rpoc, tabb, b3988, jw3951. Gene: rpoz, z5075, ecs4524. Gene: rpod.

Authors:

J.Chen,C.E.Chiu,E.A.Campbell,S.A.Darst

Key ref:

J.Chen et al. (2020). Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol Cell, 78, 275. PubMed id: 32160514 DOI: 10.1016/j.molcel.2020.02.017

Date:

13-Jul-19 Release date: 25-Mar-20

Protein chain

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

Seq: 329 a.a.

Struc: 230 a.a.

Protein chain

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

Seq: 329 a.a.

Struc: 219 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: 1345 a.a.

Protein chain

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

Seq: 91 a.a.

Struc: 75 a.a.

Protein chain

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

Seq: 613 a.a.

Struc: 548 a.a.

Protein chain

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

Seq: 329 a.a.

Struc: 73 a.a.

Protein chain

P41065  (TRAR_ECOLI) -  Protein TraR from Escherichia coli (strain K12)

Seq: 73 a.a.

Struc: 72 a.a.

DNA/RNA chains

G-C-A-C-A-A-A-T-C-C-A-T-T-G-A-C-A-A-A-A-G-A-A-G-G-C-T-A-A-A-A-G-G-G-C-A 36 bases

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

Enzyme reactions

• Enzyme class 2: Chains G, H, I, J, K, M: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chains L, N: 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: 10.1016/j.molcel.2020.02.017

Mol Cell 78:275 (2020)

PubMed id: 32160514

Stepwise Promoter Melting by Bacterial RNA Polymerase.

J.Chen, C.Chiu, S.Gopalkrishnan, A.Y.Chen, P.D.B.Olinares, R.M.Saecker, J.T.Winkelman, M.F.Maloney, B.T.Chait, W.Ross, R.L.Gourse, E.A.Campbell, S.A.Darst.

ABSTRACT

Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.