PDBsum entry 4q4z

Transcription/DNA

PDB id: 4q4z

Contents

Protein chains

231 a.a.

1112 a.a.

1494 a.a.

94 a.a.

346 a.a.

DNA/RNA

Ligands

ATP

2TM

Metals

_ZN ×2

_MG ×3

Waters ×56

PDB id:

4q4z

Name:

Transcription/DNA

Title:

Thermus thermophilus RNA polymerase de novo transcription initiation complex

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. Strain: hb8. Organism_taxid: 300852. Gene: siga, ttha0532. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Resolution:

2.90Å R-factor: 0.256 R-free: 0.275

Authors:

K.S.Murakami

Key ref:

R.S.Basu et al. (2014). Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J Biol Chem, 289, 24549-24559. PubMed id: 24973216 DOI: 10.1074/jbc.M114.584037

Date:

15-Apr-14 Release date: 30-Jul-14

Protein chains

Q9Z9H6  (RPOA_THETH) -  DNA-directed RNA polymerase subunit alpha from Thermus thermophilus

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: 1494 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: 346 a.a.

DNA/RNA chains

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

T-A-T-A-A-T-G-G-G-A-G-C-T-G-T-C-A-C-G-G-A-T-G-C-A 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: 10.1074/jbc.M114.584037

J Biol Chem 289:24549-24559 (2014)

PubMed id: 24973216

Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme.

R.S.Basu, B.A.Warner, V.Molodtsov, D.Pupov, D.Esyunina, C.Fernández-Tornero, A.Kulbachinskiy, K.S.Murakami.

ABSTRACT

The bacterial RNA polymerase (RNAP) holoenzyme containing σ factor initiates transcription at specific promoter sites by de novo RNA priming, the first step of RNA synthesis where RNAP accepts two initiating ribonucleoside triphosphates (iNTPs) and performs the first phosphodiester bond formation. We present the structure of de novo transcription initiation complex that reveals unique contacts of the iNTPs bound at the transcription start site with the template DNA and also with RNAP and demonstrate the importance of these contacts for transcription initiation. To get further insight into the mechanism of RNA priming, we determined the structure of initially transcribing complex of RNAP holoenzyme with 6-mer RNA, obtained by in crystallo transcription approach. The structure highlights RNAP-RNA contacts that stabilize the short RNA transcript in the active site and demonstrates that the RNA 5'-end displaces σ region 3.2 from its position near the active site, which likely plays a key role in σ ejection during the initiation-to-elongation transition. Given the structural conservation of the RNAP active site, the mechanism of de novo RNA priming appears to be conserved in all cellular RNAPs.