Sandbox TATA Binding Protein Austin McCauley
From Proteopedia
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== Interaction with DNA with Key Structures == | == Interaction with DNA with Key Structures == | ||
| - | The TBP is dimer, with both <scene name='60/602703/Dimer_protein/4'>monomers</scene> having the ability to interact with the DNA's TATA sequence. The TBP has a conserved core segment, C-terminal portion, of residues found in a wide range of organisms.(1) The monomer contains tertiary protein structures of both alpha helices and beta sheets. The combination of both alpha helices and beta sheets result in saddle shape. The shape of the protein plays a significant role in how it binds and interacts with DNA. The concave shape of the binding site forms from the <scene name='60/602703/Beta_sheet/1'>antiparallel beta sheet</scene> , meanwhile the the alpha helices on the non DNA binding surface interact with other transcription factors.(3)(5). The binding surface of the concave portion of the TBP has mostly | + | The TBP is dimer, with both <scene name='60/602703/Dimer_protein/4'>monomers</scene> having the ability to interact with the DNA's TATA sequence. The TBP has a conserved core segment, C-terminal portion, of residues found in a wide range of organisms.(1) The monomer contains tertiary protein structures of both alpha helices and beta sheets. The combination of both alpha helices and beta sheets result in saddle shape. The shape of the protein plays a significant role in how it binds and interacts with DNA. The concave shape of the binding site forms from the <scene name='60/602703/Beta_sheet/1'>antiparallel beta sheet</scene> , meanwhile the the alpha helices on the non DNA binding surface interact with other transcription factors.(3)(5). The binding surface of the concave portion of the TBP has mostly <scene name='60/602703/Hydrophobic_surface/1'>Hydrophobic residues</scene>. The hydrophobic residues interact with the minor groove of the DNA and place phenylalanine side chains between base pairs causing kinks.(3). The recognized mechanism for binding between TBP and DNA is an induced fit mechanism. The induced fit mechanism comes from the concave surface previously mentioned, here the minor groove and phosphate-ribose all make contact. The DNA continues to enter the binding site of the TBP as the phenylalanines partially unwind the double helix starting at the first T:A base pair of the DNA.(1) The partially unwound DNA allows for the protein to slightly bend the DNA and provides a greater interface between the DNA and protein. The greater surface area makes interactions between the TBP and DNA more favorable. TBP also demonstrates a conformational change upon binding to the DNA. When binding occurs between the DNA and TBP, the TBP twists one of its domains. The RNA polymerase complex recognizes the TBP/TFIID complex and continues transcription.(1) |
The phenylalanine residues play a key role in TBP binding to the DNA, but other residues contribute to the interaction between TBP and DNA. The following <scene name='60/602703/Residue_interaction/2'>residues interacting with TATA DNA</scene> providing stability and allow the TBP to anchor the DNA. These other interactive residues are Arg154 which contacts the sense strand backbone, and Glu 51, Lys85 and 169, and phosphates play a role in stabilizing the DNA TBP interaction.(2) Exact numbering of residues caries among organisms. | The phenylalanine residues play a key role in TBP binding to the DNA, but other residues contribute to the interaction between TBP and DNA. The following <scene name='60/602703/Residue_interaction/2'>residues interacting with TATA DNA</scene> providing stability and allow the TBP to anchor the DNA. These other interactive residues are Arg154 which contacts the sense strand backbone, and Glu 51, Lys85 and 169, and phosphates play a role in stabilizing the DNA TBP interaction.(2) Exact numbering of residues caries among organisms. | ||
Revision as of 11:05, 14 October 2014
TATA Binding Protein Structure and Funtction
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References
1. Burley, S K, and R G Roeder. "Biochemistry and Structural Biology of Transcription Factor IID (TFIID)." Annual Review of Biochemistry (1996): 769-99. Print.
2.Strahs, Daniel, Danny Barash, Xiaoliang Qian, and Tamar Schlick. "Sequence-dependent Solution Structure and Motions of 13 TATA/TBP (TATA-box Binding Protein) Complexes." Biopolymers (2003): 216-43. Print.
3.Patikoglou, G. A., J. L. Kim, L. Sun, S.-H. Yang, T. Kodadek, and S. K. Burley. "TATA Element Recognition by the TATA Box-binding Protein Has Been Conserved throughout Evolution." GENES & DEVELOPMENT (1999): 3217-230. Print.
4.Nikolov, D. B. "Crystal Structure of a Human TATA Box-binding Protein/TATA Element Complex." Proceedings of the National Academy of Sciences (1996): 4862-867. Print.
5.Nikolov, Dimitar B., and Stephen K. Burley. "2.1 Å Resolution Refined Structure of a TATA Box-binding Protein (TBP)." Nature Structural Biology (1994): 621-37. Print.
