PDBsum entry 4gzy

Transcription/DNA/RNA

PDB id: 4gzy

Contents

Protein chains

223 a.a.

1083 a.a.

1358 a.a.

93 a.a.

DNA/RNA

Metals

_MG

_ZN ×2

PDB id:

4gzy

Name:

Transcription/DNA/RNA

Title:

Crystal structures of bacterial RNA polymerase paused elongation complexes

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:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: rpoa, ttha1664. Expressed in: thermus thermophilus. Expression_system_taxid: 274. Gene: rpob, ttha1813. Gene: rpoc, ttha1812. Gene: rpoz, ttha1561.

Resolution:

3.51Å R-factor: 0.266 R-free: 0.322

Authors:

A.Weixlbaumer,K.Leon,R.Landick,S.A.Darst

Key ref:

A.Weixlbaumer et al. (2013). Structural basis of transcriptional pausing in bacteria. Cell, 152, 431-441. PubMed id: 23374340

Date:

06-Sep-12 Release date: 13-Feb-13

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: 223 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: 1083 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: 1358 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: 93 a.a.

DNA/RNA chains

A-A-G-A-G-A-T-T-C-C-C 11 bases

A-U-G-U-G-U-G-C-U 9 bases

G-G-G-A-A-T-C-T-C-T-T-C-C-A-G-C-A-C-A-C-A-T 22 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

Cell 152:431-441 (2013)

PubMed id: 23374340

Structural basis of transcriptional pausing in bacteria.

A.Weixlbaumer, K.Leon, R.Landick, S.A.Darst.

ABSTRACT

Transcriptional pausing by multisubunit RNA polymerases (RNAPs) is a key mechanism for regulating gene expression in both prokaryotes and eukaryotes and is a prerequisite for transcription termination. Pausing and termination states are thought to arise through a common, elemental pause state that is inhibitory for nucleotide addition. We report three crystal structures of Thermus RNAP elemental paused elongation complexes (ePECs). The structures reveal the same relaxed, open-clamp RNAP conformation in the ePEC that may arise by failure to re-establish DNA contacts during translocation. A kinked bridge-helix sterically blocks the RNAP active site, explaining how this conformation inhibits RNAP catalytic activity. Our results provide a framework for understanding how RNA hairpin formation stabilizes the paused state and how the ePEC intermediate facilitates termination.