PDBsum entry 5e18

Transcription/DNA/RNA

PDB id: 5e18

Contents

Protein chains

231 a.a.

1112 a.a.

1486 a.a.

94 a.a.

335 a.a.

DNA/RNA

Metals

_MG ×4

_ZN ×2

Waters ×26

PDB id:

5e18

Name:

Transcription/DNA/RNA

Title:

T. Thermophilus transcription initiation complex having a yyy discriminator sequence and a nontemplate-strand length corresponding to tss selection at position 8 (rpo-ccc-8)

Structure:

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

Source:

Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus (strain hb8 / atcc 27634 / dsm 579). Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Gene: siga, ttha0532. Expressed in: escherichia coli #1/h766. Expression_system_taxid: 469008.

Resolution:

3.30Å R-factor: 0.240 R-free: 0.284

Authors:

Y.Zhang,R.H.Ebright

Key ref:

J.T.Winkelman et al. (2016). Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science, 351, 1090-1093. PubMed id: 26941320 DOI: 10.1126/science.aad6881

Date:

29-Sep-15 Release date: 09-Mar-16

Protein chains

Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 315 a.a.

Struc: 231 a.a.

Protein chain

Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1119 a.a.

Struc: 1112 a.a.

Protein chain

Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta' from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1524 a.a.

Struc: 1486 a.a.

Protein chain

Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 99 a.a.

Struc: 94 a.a.

Protein chain

Q5SKW1  (Q5SKW1_THET8) -  RNA polymerase sigma factor SigA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 423 a.a.

Struc: 335 a.a.

DNA/RNA chains

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

C-C-C-U-C-G-A 7 bases

T-A-T-A-A-T-C-C-C-A-G-G-C-T-G-T-C-A-C-G-G-A-T-G-C 25 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

DOI no: 10.1126/science.aad6881

Science 351:1090-1093 (2016)

PubMed id: 26941320

Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.

J.T.Winkelman, I.O.Vvedenskaya, Y.Zhang, Y.Zhang, J.G.Bird, D.M.Taylor, R.L.Gourse, R.H.Ebright, B.E.Nickels.

ABSTRACT

In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.