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TitleRNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle.
Journal, issue, pagesbioRxiv, Year 2026
Publish dateApr 7, 2026
AuthorsYukti Dhingra / Robert Landick / Elizabeth A Campbell / Seth A Darst /
PubMed AbstractThe nucleotide-addition cycle (NAC) of multi-subunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the ...The nucleotide-addition cycle (NAC) of multi-subunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the trigger loop (TL). The TL is open (unfolded) in most RNAP structures but can close (fold) in substrate-bound (post- or pre-translocated) states of the RNAP, promoting catalysis. TL closure has been associated with closure of another conserved structural element, the Rim-Helices/F-loop (RH-FL), but the role of the RH-FL in the NAC is unclear. Antibiotic leads CBR9379 and AAP-SO inhibit the and RNAPs, respectively, by binding in a pocket formed by the bridge helix and RH-FL. The precise mechanism of action for these inhibitors is yet to be defined. We present cryo-electron microscopy structures showing that both compounds inhibit the RNAP NAC by preventing RH-FL closure, thereby allosterically destabilizing the closed TL. This work reveals a conserved mechanistic principle of RNAP catalysis across all domains of life and provides new insight for antibiotic design.
External linksbioRxiv / PubMed:41993335 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.0 Å
Structure data

75279

10ma

EMDB-75279, PDB-10ma:
Closed Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with a closed active site (closed TL, SI3 and RH-FL)
Method: EM (single particle) / Resolution: 2.9 Å

75280

10mb

EMDB-75280, PDB-10mb:
Open1 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL)
Method: EM (single particle) / Resolution: 2.9 Å

75281

10mc

EMDB-75281, PDB-10mc:
Open2 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL)
Method: EM (single particle) / Resolution: 2.8 Å

75282

10md

EMDB-75282, PDB-10md:
Open3 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL)
Method: EM (single particle) / Resolution: 2.8 Å

75283

10me

EMDB-75283, PDB-10me:
SemiClosed Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with a semi-closed active site (closed TL and SI3, open RH-FL)
Method: EM (single particle) / Resolution: 4.0 Å

75284

10mf

EMDB-75284, PDB-10mf:
CBR9379 bound Open1 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL)
Method: EM (single particle) / Resolution: 2.8 Å

75285

10mg

EMDB-75285, PDB-10mg:
CBR9379 bound Open2 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL)
Method: EM (single particle) / Resolution: 2.9 Å

75286

10mi

EMDB-75286, PDB-10mi:
Closed Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with a closed active site (closed TL and RH-FL)
Method: EM (single particle) / Resolution: 3.0 Å

75287

10mj

EMDB-75287, PDB-10mj:
Open Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with an open active site (open TL and RH-FL)
Method: EM (single particle) / Resolution: 3.3 Å

75288

10mk

EMDB-75288, PDB-10mk:
SemiClosed Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with a semiclosed active site (closed TL, open RH-FL)
Method: EM (single particle) / Resolution: 3.3 Å

75289

10ml

EMDB-75289, PDB-10ml:
AAP-SO2 bound Open Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with an open active site (open TL and RH-FL)
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-1N7:
CHAPSO / detergent*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-42T:
3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

PDB-1bnv:
CARBONIC ANHYDRASE II INHIBITOR

Source
  • escherichia coli (E. coli)
  • mycobacterium tuberculosis (bacteria)
KeywordsTranscription/DNA/RNA / Transcription / DNA/RNA / Nucleotide addition cycle / RNA polymerase / Transcription-DNA-RNA complex

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