PDBsum entry 6lts

Transcription

PDB id: 6lts

Contents

Protein chains

226 a.a.

1111 a.a.

1486 a.a.

94 a.a.

336 a.a.

DNA/RNA

Metals

_MG ×5

_ZN ×2

PDB id:

6lts

Name:

Transcription

Title:

Crystal structure of thermus thermophilus transcription initiation complex comprising a truncated sigma finger

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 hb8. Organism_taxid: 300852. Strain: hb8. Gene: siga, ttha0532. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Thermus thermophilus. Organism_taxid: 274.

Resolution:

3.45Å R-factor: 0.221 R-free: 0.258

Authors:

Y.Zhang,R.H.Ebright

Key ref:

L.Li et al. (2020). RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Proc Natl Acad Sci U S A, 117, 5801-5809. PubMed id: 32127479 DOI: 10.1073/pnas.1920747117

Date:

23-Jan-20 Release date: 11-Mar-20

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: 226 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: 1111 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: 336 a.a.

DNA/RNA chains

T-A-T-A-A-T-G-G-G-A-G-C-T-G-T-C-A-C-G-G-A-T-G-C 24 bases

G-C-A-T-C-C-G-T-G-A 10 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: 10.1073/pnas.1920747117

Proc Natl Acad Sci U S A 117:5801-5809 (2020)

PubMed id: 32127479

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.

L.Li, V.Molodtsov, W.Lin, R.H.Ebright, Y.Zhang.

ABSTRACT

All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.