TATA BINDING PROTEINS

Presented by: Pragya PrasannaPhD Biotechnology

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)

• General transcription factors combinewith RNA polymerase to form apreinitiation complex

• The assembly of preinitiationcomplexes involving polymerase IIis quite complex

11-4

Model of Formation of the DABPolF Complex

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

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

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

TBPs saddle-structure

DNA

protein

Concaveinside

Convexsurface

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

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 wayNot like this

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

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

Thank You