PDBsum entry 6b6h

Transcription/transferase/DNA/RNA

PDB id: 6b6h

Contents

Protein chains

230 a.a.

1340 a.a.

1337 a.a.

79 a.a.

497 a.a.

201 a.a.

75 a.a.

DNA/RNA

Ligands

CMP ×2

Metals

_MG

_ZN ×2

PDB id:

6b6h

Name:

Transcription/transferase/DNA/RNA

Title:

The cryo-em structure of a bacterial class i transcription activation 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 o157:h7. Organism_taxid: 83334. Gene: rpoa, z4665, ecs4160. Expressed in: escherichia coli. Expression_system_taxid: 562. Escherichia coli o45:k1 (strain s88 / expec). Organism_taxid: 585035. Strain: s88 / expec. Gene: rpob, ecs88_4448.

Authors:

B.Liu,C.Hong,R.Huang,Z.Yu,T.A.Steitz

Key ref:

B.Liu et al. (2017). Structural basis of bacterial transcription activation. Science, 358, 947-951. PubMed id: 29146813 DOI: 10.1126/science.aao1923

Date:

02-Oct-17 Release date: 15-Nov-17

Protein chains

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

Seq: 329 a.a.

Struc: 230 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: 1337 a.a.

Protein chain

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

Seq: 91 a.a.

Struc: 79 a.a.

Protein chain

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

Seq: 613 a.a.

Struc: 497 a.a.

Protein chains

P0ACJ8  (CRP_ECOLI) -  DNA-binding transcriptional dual regulator CRP from Escherichia coli (strain K12)

Seq: 210 a.a.

Struc: 201 a.a.

Protein chain

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

Seq: 329 a.a.

Struc: 75 a.a.

DNA/RNA chains

T-A-A-A-A-T-G-T-G-A-T-C-T-A-G-A-T-C-A-C-A-T-T-T-T-A-G-G-C-A-A-A-A-A-A-G-G-C-C- 88 bases

C-G-C-C-G-C-G-T-C-A-G-A-C-T-C-G-T-A-G-G-A-T-T-A-T-A-G-C-A-T-A-C-G-T-G-A-G-G-T- 88 bases

GTP-A-G 3 bases

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D, E, I: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: Chains F, G, H: 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: 10.1126/science.aao1923

Science 358:947-951 (2017)

PubMed id: 29146813

Structural basis of bacterial transcription activation.

B.Liu, C.Hong, R.K.Huang, Z.Yu, T.A.Steitz.

ABSTRACT

In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo-electron microscopy structure of an intactEscherichia coliclass I TAC containing a CAP dimer, a σ⁷⁰-RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism.