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Abstract:
RNA polymerase (Pol) II consists of a 10-polypeptide catalytic core
and the two-subunit Rpb47 complex that is required for transcription
initiation. Previous structures of the Pol II core revealed a
‘‘clamp,’’ which binds the DNA template strand via three ‘‘switch
regions,’’ and a flexible ‘‘linker’’ to the C-terminal repeat domain
(CTD). Here we derived a model of the complete Pol II by fitting
structures of the core and Rpb47 to a 4.2-Å crystallographic
electron density map. Rpb47 protrudes from the polymerase
‘‘upstream face,’’ on which initiation factors assemble for promoter
DNA loading. Rpb7 forms a wedge between the clamp and the
linker, restricting the clamp to a closed position. The wedge
allosterically prevents entry of the promoter DNA duplex into the
active center cleft and induces in two switch regions a conformation
poised for template-strand binding. Interaction of Rpb47
with the linker explains Rpb4-mediated recruitment of the CTD
phosphatase to the CTD during Pol II recycling. The core–Rpb7
interaction and some functions of Rpb47 are apparently conserved
in all eukaryotic and archaeal RNA polymerases but not in
the bacterial enzyme.
