Clegg TBP sandbox: Difference between revisions
Wally Novak (talk | contribs) New page: left|200px {{STRUCTURE_1cdw| PDB=1cdw | SCENE= }} ===HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA=== The TATA box-binding protein (TBP) is required by all three euk... |
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=== | ==TATA Binding Protein Overview== | ||
In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC starts with the Tata Binding Protein (TBP) binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref>Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).</ref>’ This mechanism/assembly enables the start of transcription. | |||
==General Structure of TBP== | |||
The TBP has two imperfect direct repeats that form a <scene name='Clegg_TBP_sandbox/Saddle/1'>saddle</scene> shaped structure with <scene name='Clegg_TBP_sandbox/Stirrup/2'>stirrups</scene> forming a concave like DNA binding surface. This allows for an induced-fit mechanism. The imperfect direct repeats differ by two residues. The first is a deletion of a residue at the end of helix H2. The second is the addition of a proline in helix H2' that enables a <scene name='Clegg_TBP_sandbox/Proline/1'>bend</scene> that does not occur on H2.‘<ref>Crystal structure of a human TATA box-binding protein/TATA element complex., Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK, Proc Natl Acad Sci U S A. 1996 May 14;93(10):4862-7. PMID:8643494</ref>’ | |||
==TBP-DNA Interactions== | |||
When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/3'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.961</ref>’ As a result the DNA is partially unwound between the two sets of Phenylalanines causing the minor groove to be widened.‘<ref>X-ray crystallographic studies of eukaryotic transcription initiation factors. Burley SK., Philosiphical Transactions of the Royal Society of London series B-Biol Sci. 1996 April 29 . 51: 1339; 483-489 10.1098/rstb.1996.0046</ref>’A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which eventually leads to transcripton. | |||
==Reference== | ==Reference== | ||
<references/> | |||
Latest revision as of 19:01, 26 November 2012
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| 1cdw, resolution 1.90Å () | |||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
TATA Binding Protein OverviewTATA Binding Protein Overview
In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC starts with the Tata Binding Protein (TBP) binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘[1]’ This mechanism/assembly enables the start of transcription.
General Structure of TBPGeneral Structure of TBP
The TBP has two imperfect direct repeats that form a shaped structure with forming a concave like DNA binding surface. This allows for an induced-fit mechanism. The imperfect direct repeats differ by two residues. The first is a deletion of a residue at the end of helix H2. The second is the addition of a proline in helix H2' that enables a that does not occur on H2.‘[2]’
TBP-DNA InteractionsTBP-DNA Interactions
When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a , approximately 44 degrees, within the TATA box.‘[3]’ As a result the DNA is partially unwound between the two sets of Phenylalanines causing the minor groove to be widened.‘[4]’A total of seven residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: , Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which eventually leads to transcripton.
ReferenceReference
- ↑ Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).
- ↑ Crystal structure of a human TATA box-binding protein/TATA element complex., Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK, Proc Natl Acad Sci U S A. 1996 May 14;93(10):4862-7. PMID:8643494
- ↑ Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.961
- ↑ X-ray crystallographic studies of eukaryotic transcription initiation factors. Burley SK., Philosiphical Transactions of the Royal Society of London series B-Biol Sci. 1996 April 29 . 51: 1339; 483-489 10.1098/rstb.1996.0046