molecular biology

1. TATA BINDING PROTEINS
Presented by: Pragya Prasanna
PhD Biotechnology

2. Transcription in Eukaryotes
• Eukaryotic RNA polymerases, unlike their
bacterial counterparts, are incapable of binding
by themselves to their respective promoters
• Eukaryotic RNA polymerases rely on proteins
called transcription factors to show them the
way
• Two classes: general transcription factors and
gene-specific transcription factors (activators)

3. • General transcription factors combine
with RNA polymerase to form a
preinitiation complex
• The assembly of preinitiation
complexes involving polymerase II
is quite complex

4. 11-4
Model of Formation of the DABPolF Complex

5. Structure and Function of TFIID
TFIID contains several subunits
– TATA-box binding protein (TBP)
• Highly evolutionarily conserved
• Binds to the minor groove of the TATA box
–Saddle-shaped TBP lines up with DNA
–Underside of the saddle forces open the
minor groove
–The TATA box is bent into 80° curve
– TBP-associated factors (TAFs) specific for class II

6. TBP [TFIID] function
• Binds TATA - main sequence recognition
event during
Binds a variety of different TATA-like sequences
– A slow binding reaction
– minor groove contact
– binds as monomer
• Affinity of TBP for TATA contributes to
promoter strength
• Binds also several other polypeptides
– activators (Sp1, Tax1, E1A)
– TAFs (dTAF110, dTAF40)
– GTFs (TFIIB, TFIIA)
– inhibitors
• TBP = universal TF involved in all three pol
syst.
– TBP i SL1, TFIID, TFIIIB
DNA
Other factors
N

7. TBP versus TFIID
• Subunit-structure
– TFIID = TBP + multiple TAFs
– mammalian TFIID: 750 kDa (II), 300 kDa (III) and 200 kDa (I)
– TBP only a small core in the TFIID complex
• human 38 kDa, yeast 27 kDa, Arabidopsis 22 kDa
– TBP = N-term divergent domain + C-term. conserved domain
• C-term domain 180aa
• Carries all essential functions
• N-term domain divergent
TAFs
TBP
N

8. TBPs saddle-structure
DNA
protein
Concave
inside
Convex
surface
3D: saddle-structure
• Twofold symmetry -form of a saddle.
• Concave inside binds DNA in minor groove
through a 10-stranded antiparallel -sheet
• Convex surface binds other GTFs via 4 -helixes
• loop (“stirrup”) on each side with Phe side-
chains intercalating in DNA

9. TBPs effect on DNA
• DNA-structure is distorted upon TBP binding
– DNA severely bended, unwinded and distorted
– DNA shaped by TBP´s -sheet
– The intercalating Phe-residues contributes to kink
• Effect?
– Upstream and downstream elements brought closes together
– incompatible with nucleosome structure
.. but this way
Not like this

10. A Two-Step Mechanism of TBP
Binding to DNA
• First step
– Full-length TBPWT first binds
to TATA box to form an
unbent TBP-TATA box
complex.
• Second step
– Then, this unbent complex
slowly forms the bent TBP-
TATA box complex.
– TFIIB can directly recognize
the unbent and/or bent
TBP-TATA-complexes to form
the bent TBP-TATA box
complex.

11. 11-11
The Versatility of TBP
• Genetic studies have demonstrated TBP
mutant cell extracts are deficient in:
– Transcription of class II genes
– Transcription of class I and III genes
• TBP is a universal transcription factor required
by all three classes of genes
• Required in transcription of at least some
genes of Archaea, single-celled organisms
lacking nuclei

12. Thank You