Human TFIIB in the TFIIB-TBP-TATA-Element
Josh Cowgill '08, Nick Fanning
'08 and Albert Coombs III '07
TFIIB is a eukaryotic general transcription factor
(GTF) that is necessary for both RNA polymerase II promoter binding and promoter
clearance. With regard to only the necessary GTF's, TFIID, which contains
TATA binding protein (TBP), binds the TATA-element
on DNA and starts the formation of the transcriptional pre-initiation complex.
TFIIB binds next, and together the DNA, TBP,
and TFIIB form a molecular binding platform that
is recognized by RNA polymerase II. In this ternary complex, the role of TFIIB
is to bind both the DNA and TBP to create stabilizing
II. TFIIB General Structure
The protein's N-terminal portion contains a putative Zinc-binding
sequence that plays a major role in the successful binding of RNA polymerase
II. This N-terminal region does not, however, have a very large role in
this ternary complex and thus is not shown here. Core TFIIB, on the other
hand, is extremely important to this ternary complex, and it has a two-domain
. The core region/C-terminal region together consist of two 84-amino-acid
direct repeats. Overall, the protein has dimensions of 65A x 32A x 32A.
III. Core TFIIB Specifics
As previously mentioned, core TFIIB has two nearly identical domains,
which are connected by a short
and rotated by 90 degrees with respect to one another. Each domain consists
of five alpha-helices (domain I has helices BH1-BH5, while domain II has
helices BH1'-BH5') arranged in a compact globular fashion with BH3/BH3'
in the hydrophobic core
. Just past BH5' in the C-terminal direction is the short alpha helix BH6'
and a random coil segment that extends to the molecule's C-terminus
. These two structures form the molecule's C-terminal region and have no
analogs in domain I. The solitary molecule is held together by limited interdomain
hydrophobic interactions between residues
in BH4 and the BH4'-BH5' loop and between residues
in BH1' and the BH3-BH4 loop
IV. Interactions of the Ternary Complex
TBP binds DNA at the TATA-element,
and as a subunit of TFIID it is the first protein to bind DNA during eukaryotic
transcription initiation. TBP recognizes the
TATA-element via an induced-fit mechanism where beta-sheets
on TBP insert into the DNA's minor groove
residues near these beta-sheets
intercalate between bases in the DNA and cause two distinct kinks
. These kinks generate a sterically favorable complementary interaction
surface for TBP and the DNA.
It is this TBP-TATA-element complex
that is recognized by TFIIB. TFIIB
acts as a clamp holding TBP tightly to the
. It does this by binding TBP in its cleft
between the plane of beta-sheets and alpha-helices and by binding backbones
of both coding and non-coding DNA upstream and downstream of the TATA-element
(see section V for specifics). This binding is non-sequence specific because
TFIIB does not contact any of the DNA bases.
Overall ternary complex stability comes from favorable Van der Waals and
electrostatic interactions between TFIIB and
the TBP-TATA-element complex.
V. TFIIB Specifics in the Ternary Complex
As previously mentioned, TFIIB binds
the DNA backbone of the coding region and non-coding region both upstream
and downstream of the TATA-element in a non-sequence specific manner
. It does this by using many positively
charged basic residues to form charge-charge interactions with the
negatively charged DNA backbone
. As we will see later on, many basic residues of TFIIB
also interact with the acidic C-terminal stirrup
. In the ternary complex overall, this positive charge provided by TFIIB
helps to cancel much of the negative charge of the acidic C-terminal stirrup
and the negative charge of the DNA backbone, thus greatly stabilizing the
The so-called "C-terminal stirrup" of TBP
constitutes the primary binding site for TFIIB
in this ternary complex. Residues 143-147 on the stirrup form salt bridges,
hydrogen bonds, and Van der Waals contacts with at least ten TFIIB
residues. Residues on TBP are listed in red,
residues on TFIIB are listed in blue,
and all residues are displayed in white.
On the C-terminal stirrup alone, Glu146-->
Lys188 form a salt bridge
; Glu144--> Arg169,
and Glu146--> Phe177
form hydrogen bonds
, while Tyr143--> Leu208,
and Leu147--> Gly192
all make Van der Waals contacts
In addition to the C-terminal stirrup, residues on TBP's
alpha-helix H1' also interact with at least two residues on TFIIB.
form a hydrogen bond
, while Glu131--> Leu208
and Tyr135--> Leu208
form Van der Waals contacts
. Finally, Lys197, located near TBP's
C-terminus, forms a salt bridge with TFIIB's
The overall purpose of TFIIB in this
ternary complex is to stabilize TBP to the
TATA-element DNA and to create a stable binding platform for RNA polymerase
II. Perhaps an even more interesting region of TFIIB
is its N-terminal zinc-ribbon. The N-terminus plays a huge role in RNA polymerase
II binding and promoter clearance. We believe that we know most of the functions
of this region, but the crystal structure of this region on human TFIIB
has not yet been determined.
Kosa PF, Ghosh G, DeDecker BS, and Sigler PB. The 2.1-A
crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription
factor (II)B core/TATA-box. Proc Natl Acad Sci USA. 1997. 94(12): 6042-6047.
Nikolov DB, Chen H, Halay ED, Usheva AA, Hisatake
K, Lee DK, Roeder RG, and Burley SK. Crystal structure of a TFIIB-TBP-TATA-element
ternary complex. Nature. 1995. 377: 119-128.
Nikolov DB, Chen H, Hoffman A, Halay ED, Roeder RG,
and Burley SK. Crystal structure of a human TATA box-binding protein/TATA
element complex. Proc Natl Acad Sci USA.. 1996. 93(10): 4862-4867.
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