In eukaryotes the initiation of transcription of protein encoding genes by the
polymerase II complexe (Pol II) is modulated by general and specific
transcription factors. The general transcription factors operate through
common promoters elements (such as the TATA box). At least seven different
proteins associate to form the general transcription factors: TFIIA, -IIB,
-IID, -IIE, -IIF, -IIG, and -IIH .
TFIIB and TFIID are responsible for promoter recognition and interaction with
pol II; together with Pol II, they form a minimal initiation complex, capable
of transcription under certain conditions. The TATA box of a Pol II promoter
is bound in the initiation complex by the TBP subunit of TFIID, which bends
the DNA around the C-terminal domain of TFIIB (see <PDOC00624>) whereas the
N-terminal zinc finger of TFIIB interacts with Pol II [2,3].
The TFIIB zinc finger adopts a zinc ribbon fold characterized by two
β-haipins forming two structurally similar zinc-binding sub-sites (see
<PDB:1PFT>) . The zinc finger contacts the rbp1 subunit of Pol II through
its dock domain, a conserved region of about 70 amino acids located close to
the polymerase active site [5,6]. In the Pol II complex this surface is
located near the RNA exit groove . Interestingly this sequence is best
conserved in the three polymerases that utilize a TFIIB-like general
transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in
Pol I .
The profile we developed covers the whole TFIIB zinc finger.
June 2005 / First entry.
PROSITE method (with tools and information) covered by this documentation:
The basic RNA polymerase II transcriptional machinery.
PROSITE is copyright. It is produced by the SIB Swiss Institute
Bioinformatics. There are no restrictions on its use by non-profit
institutions as long as its content is in no way modified. Usage by and
for commercial entities requires a license agreement. For information
about the licensing scheme send an email to
or see: prosite_license.html.