4GZZ: Crystal structures of bacterial RNA Polymerase paused elongation complexes

Citation:
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.
PDB ID: 4GZZDownload
MMDB ID: 107614
PDB Deposition Date: 2012/9/6
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 4.2927  Å
Source Organism:
Thermus thermophilus HB8
Similar Structures:
Biological Unit for 4GZZ: octameric; determined by author and by software (PISA)
Molecular Components in 4GZZ
Label Count Molecule
Proteins (5 molecules)
2
DNA-directed RNA Polymerase Subunit Alpha(Gene symbol: TTHA1664)
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta(Gene symbol: rpoB)
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta'(Gene symbol: TTHA1812)
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Omega(Gene symbol: rpoZ)
Molecule annotation
Nucleotides(3 molecules)
1
Non-template DNA
Molecule annotation
1
RNA Transcript
Molecule annotation
1
Template DNA
Molecule annotation
Chemicals (3 molecules)
1
2
2
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.