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Structure paper

TitleStructures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.
Journal, issue, pagesNature, Vol. 565, Issue 7739, Page 382-385, Year 2019
Publish dateJan 9, 2019
AuthorsHande Boyaci / James Chen / Rolf Jansen / Seth A Darst / Elizabeth A Campbell /
PubMed AbstractA key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex. To generate the open complex, the conserved catalytic core of the RNAP combines ...A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex. To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed. Here we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including structures of partially melted intermediates. The structures show that late steps of promoter melting occur within the RNAP cleft, delineate key roles for fork-loop 2 and switch 2-universal structural features of RNAP-in restricting access of DNA to the RNAP active site, and explain why clamp opening is required to allow entry of single-stranded template DNA into the active site. The key roles of fork-loop 2 and switch 2 suggest a common mechanism for late steps in promoter DNA opening to enable gene expression across all domains of life.
External linksNature / PubMed:30626968 / PubMed Central
MethodsEM (single particle)
Resolution3.55 - 4.4 Å
Structure data

9037

6edt

EMDB-9037, PDB-6edt:
Mycobacterium tuberculosis RNAP open promoter complex with RbpA/CarD and AP3 promoter
Method: EM (single particle)

9039

6ee8

EMDB-9039, PDB-6ee8:
Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter
Method: EM (single particle) / Resolution: 3.92 Å

9041

6eec

EMDB-9041, PDB-6eec:
Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin
Method: EM (single particle) / Resolution: 3.55 Å

9047

6m7j

EMDB-9047, PDB-6m7j:
Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin
Method: EM (single particle) / Resolution: 4.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-C0L:
methyl

Source
  • mycobacterium tuberculosis (bacteria)
  • synthetic construct (others)
KeywordsTRANSCRIPTION/DNA / initiation / transcription bubble / closed clamp / open promoter complex / TRANSCRIPTION / TRANSCRIPTION-DNA complex / half bubble / intermediate

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