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Structure paper

TitleDirect binding of TFEα opens DNA binding cleft of RNA polymerase.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 6123, Year 2020
Publish dateNov 30, 2020
AuthorsSung-Hoon Jun / Jaekyung Hyun / Jeong Seok Cha / Hoyoung Kim / Michael S Bartlett / Hyun-Soo Cho / Katsuhiko S Murakami /
PubMed AbstractOpening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron ...Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.
External linksNat Commun / PubMed:33257704 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.6 - 3.97 Å
Structure data

PDB-6kf3:
Cryo-EM structure of Thermococcus kodakarensis RNA polymerase
Method: ELECTRON MICROSCOPY / Resolution: 3.9 Å

PDB-6kf4:
Cryo-EM structure of Thermococcus kodakarensis RNA polymerase
Method: ELECTRON MICROSCOPY / Resolution: 3.97 Å

PDB-6kf9:
Cryo-EM structure of Thermococcus kodakarensis RNA polymerase
Method: ELECTRON MICROSCOPY / Resolution: 3.79 Å

PDB-6pln:
X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-6xjf:
X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha (SeMet labeled protein)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • thermococcus kodakarensis (strain atcc baa-918 / jcm 12380 / kod1) (archaea)
  • thermococcus kodakarensis kod1 (archaea)
  • pyrococcus furiosus (archaea)
  • pyrococcus furiosus (strain atcc 43587 / dsm 3638 / jcm 8422 / vc1) (archaea)
KeywordsTRANSCRIPTION / apo-RNA polymerase / TFE / general transcription factor

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