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TitleMycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 6419, Year 2020
Publish dateDec 18, 2020
AuthorsTomáš Kouba / Tomáš Koval' / Petra Sudzinová / Jiří Pospíšil / Barbora Brezovská / Jarmila Hnilicová / Hana Šanderová / Martina Janoušková / Michaela Šiková / Petr Halada / Michal Sýkora / Ivan Barvík / Jiří Nováček / Mária Trundová / Jarmila Dušková / Tereza Skálová / URee Chon / Katsuhiko S Murakami / Jan Dohnálek / Libor Krásný /
PubMed AbstractRNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism ...RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids.
External linksNat Commun / PubMed:33339823 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2 - 3.36 Å
Structure data

EMDB-10996, PDB-6yxu:
Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State I, primary channel engaged
Method: EM (single particle) / Resolution: 3.08 Å

EMDB-11004, PDB-6yys:
Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interfering
Method: EM (single particle) / Resolution: 3.08 Å

EMDB-11026, PDB-6z11:
Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State III, primary channel dis-engaged and active site interfering
Method: EM (single particle) / Resolution: 3.36 Å

PDB-6vsx:
X-ray crystal structure of the C-terminal domain of Bacillus subtilis RNA polymerase binding helicase HelD
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-HOH:
WATER / Water

ChemComp-ZN:
ZINC ION / Zinc

ChemComp-MG:
MAGNESIUM ION / Magnesium

Source
  • mycolicibacterium smegmatis mc2 155 (bacteria)
  • bacillus subtilis (bacteria)
KeywordsBacterial Proteins / Catalytic Domain / Cryoelectron Microscopy / DNA, Bacterial / DNA-Directed RNA Polymerases / Models, Molecular / Mycobacterium smegmatis / Nucleic Acids / Protein Binding / Protein Domains / TRANSCRIPTION / RNA polymerase / Helicase / transcription cycle helicase-like protein RNA polymerase / trasncription / transcription cycle helicase-like protein RNA polymerase transcription

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