Sandbox TATA Binding Protein Austin McCauley

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Revision as of 02:24, 14 October 2014

TATA Binding Protein Structure and Funtction

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function

TATA binding protein(TBP) is one of several proteins which make up the RNA polymerase complex used in transcription. Specifically the TBP belongs to the TFIID complex containing a variety of transcription factors contributing to success of transcription for the RNA polymerase complex. TBP is involved in all three RNA polymerase complexes, making TBP an essential initiation factor in transcription. (BIOCHEMISTRY AND STRUCTURAL BIOLOGY OF TRANSCRIPTION FACTOR IID (TFIID)) The TFIID focuses on binding to the DNA used in transcription. The TBP's main function is to bind with the TATA box of the DNA in order to anchor the protein to the TFIID complex, thus allowing for RNA II polymerase to carry out transcription. (TATA element recognition by the TATA box-binding protein has been conserved throughout evolution) The importance of the TBP in the RNA polymerase complex stems from the RNA polymerase complex's inability to recognize the target promoter directly. The TBP binds to the TATA sequence approximately 25 base pairs upstream the start site of the DNA.(BIOCHEMISTRY AND STRUCTURAL BIOLOGY OF TRANSCRIPTION FACTOR IID (TFIID))

Interaction with DNA with Key Structures

The TBP is dimer, with both monomers having the ability to interact with the DNA's TATA sequence. The TBP has a conserved core segment of residues found in a wide range of organisms.(Biochemistry and structural biology of transcription factor IID (TFIID).) 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 antiparallel beta sheet, meanwhile the the alpha helices on the non DNA binding surface interact with other transcription factors.(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317201/)(2.1 A resolution refined structure of a TATA box-binding protein (TBP)). The binding surface of the concave portion of the TBP has mostly hydrophobic residues. The hydrophobic residues interact with the minor groove of the DNA and place phenylalanine side chains between base pairs causing kinks.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317201/)

Structural highlights

References

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

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Sandbox TATA Binding Protein Austin McCauley

From Proteopedia

Revision as of 02:24, 14 October 2014

TATA Binding Protein Structure and Funtction

Function

Interaction with DNA with Key Structures

Structural highlights

References

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 == Function ==
 TATA binding protein(TBP) is one of several proteins which make up the RNA polymerase complex used in transcription. Specifically the TBP belongs to the TFIID complex containing a variety of transcription factors contributing to success of transcription for the RNA polymerase complex. TBP is involved in all three RNA polymerase complexes, making TBP an essential initiation factor in transcription. (BIOCHEMISTRY AND
-STRUCTURAL BIOLOGY OF
+STRUCTURAL BIOLOGY OF TRANSCRIPTION FACTOR IID (TFIID)) The TFIID focuses on binding to the DNA used in transcription. The TBP's main function is to bind with the TATA box of the DNA in order to anchor the protein to the TFIID complex, thus allowing for RNA II polymerase to carry out transcription. (TATA element recognition by the TATA box-binding protein has been conserved throughout evolution) The importance of the TBP in the RNA polymerase complex stems from the RNA polymerase complex's inability to recognize the target promoter directly. The TBP binds to the TATA sequence approximately 25 base pairs upstream the start site of the DNA.(BIOCHEMISTRY AND STRUCTURAL BIOLOGY OF TRANSCRIPTION FACTOR IID (TFIID))
-TRANSCRIPTION FACTOR IID
-(TFIID)) The TFIID focuses on binding to the DNA used in transcription. The TBP's main function is to bind with the TATA box of the DNA in order to anchor the protein to the TFIID complex, thus allowing for RNA II polymerase to carry out transcription. (TATA element recognition by the TATA box-binding protein has been conserved throughout evolution) The importance of the TBP in the RNA polymerase complex stems from the RNA polymerase complex's inability to recognize the target promoter directly. The TBP binds to the TATA sequence approximately 25 base pairs upstream the start site of the DNA.(BIOCHEMISTRY AND
-STRUCTURAL BIOLOGY OF
-TRANSCRIPTION FACTOR IID
-(TFIID))
 == Interaction with DNA with Key Structures ==
- The TBP is dimer, with both monomers having the ability to interact with the DNA's TATA sequence. The TBP has a conserved core segment of residues found in a wide range of organisms.(Biochemistry and structural biology of transcription factor IID (TFIID).) 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 antiparallel beta sheet, meanwhile the the alpha helices on the non DNA binding surface interact with other transcription factors. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317201/)(2.1 A resolution refined structure of a TATA box-binding protein (TBP)). The binding surface of the concave portion of the TBP has mostly hydrophobic
+The TBP is dimer, with both monomers having the ability to interact with the DNA's TATA sequence. The TBP has a conserved core segment of residues found in a wide range of organisms.(Biochemistry and structural biology of transcription factor IID (TFIID).) 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 antiparallel beta sheet, meanwhile the the alpha helices on the non DNA binding surface interact with other transcription factors.(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317201/)(2.1 A resolution refined structure of a TATA box-binding protein (TBP)). The binding surface of the concave portion of the TBP has mostly hydrophobic residues. The hydrophobic residues interact with the minor groove of the DNA and place phenylalanine side chains between base pairs causing kinks.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317201/)
 == Structural highlights ==