Proteopedia - User contributions [en]

Yeast TATA Binding Protein

2013-11-25T19:22:50Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>

== Overview ==
The 2.5 Å crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/5'>β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are <scene name='56/567282/Basic_residues_of_tbp/2'>two rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site, <scene name='56/567282/Phe_interacting_with_dna4/2'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/2'>Lys 133, 145, 151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T04:29:36Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T04:18:33Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>

== Overview ==
The 2.5 Å crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/5'>β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are <scene name='56/567282/Basic_residues_of_tbp/2'>two rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site, <scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/2'>Lys 133, 145, 151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T04:07:17Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/5'>β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are <scene name='56/567282/Basic_residues_of_tbp/2'>two rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T04:05:00Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/4'>β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are <scene name='56/567282/Basic_residues_of_tbp/2'>two rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T03:54:03Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are <scene name='56/567282/Basic_residues_of_tbp/2'>two rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T03:49:42Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T03:49:19Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T03:48:31Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/2'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T03:45:49Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic <scene name='56/567282/Saddle-shape/1'>saddle-shape</scene> consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T03:27:03Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. <ref name=Berg/> TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. <ref name=Berg/> During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. <ref name=Berg/> The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. <ref name=Berg/> The surface of the TBP saddle provides docking sites for the binding of other transcription factors. <ref name=Berg/> TFIIA is recruited and interacts primarily with the TBP. <ref name=Berg/> TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus. <ref name=Berg/>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-21T03:25:05Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic/2'>hydrophobic under-surface of the TBP saddle</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe_interacting_with_dna4/1'>four Phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

==Role as Transcription Factor Subunit==
TBP acts as a 30-kd subunit of the 700-kd eukaryotic transcription factor TFIID. TBP and a variety of TBP-associated factors, make up the TFIID, which in turn makes up part of the RNA polymerase II preinitiation complex. During the formation of the preinitiation transcription complex of RNA polymerase II, TFIID is the first protein to bind to DNA. The recruitment of other factors required for RNA Polymerase II to initiate transcription results from the binding of TFIID to the TATA box in the promoter region of the gene. The surface of the TBP saddle provides docking sites for the binding of other transcription factors. TFIIA is recruited and interacts primarily with the TBP. TFIIB and TFIIF are recruited and are followed by the RNA polymerase II, TFIIE, and TFIIH. This results in the formation of the basal transcription apparatus.

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-04T20:16:14Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by TBP of the <scene name='56/562422/Tata_binding_tata/2'> TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic_orange/1'>hydrophobic under-surface of the TBP saddle.</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe/1'>four phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-04T19:22:30Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by <scene name='56/562422/Tata_binding_tata/2'> TBP of the TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. <ref name=Berg/> TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. <ref name=Berg/> TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. <ref name=Kim/> On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. <ref name=Berg/> The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic_orange/1'>hydrophobic under-surface of the TBP saddle.</scene> <ref name=Berg/> At the binding site,<scene name='56/567282/Phe/1'>four phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. <ref name=Berg/> The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA. <ref name=Kook>PMID:7738039</ref>

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-04T19:17:59Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by <scene name='56/562422/Tata_binding_tata/2'> TBP of the TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. TBP is a 30-kd component of the 700-kd TFIID complex. <ref name=Berg/> TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. <ref name=Chasman/> TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> <ref name=Kim/> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface. <ref name=Chasman/>

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic_orange/1'>hydrophobic under-surface of the TBP saddle.</scene> At the binding site,<scene name='56/567282/Phe/1'>four phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA.

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-04T19:15:43Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by <scene name='56/562422/Tata_binding_tata/2'> TBP of the TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. TBP is a 30-kd component of the 700-kd TFIID complex. TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Chasman>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface.

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic_orange/1'>hydrophobic under-surface of the TBP saddle.</scene> At the binding site,<scene name='56/567282/Phe/1'>four phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA.

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-04T19:14:57Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by <scene name='56/562422/Tata_binding_tata/2'> TBP of the TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. TBP is a 30-kd component of the 700-kd TFIID complex. TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. <ref name=Kim>PMID:008367480</ref> Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface.

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic_orange/1'>hydrophobic under-surface of the TBP saddle.</scene> At the binding site,<scene name='56/567282/Phe/1'>four phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. <ref name=Kim/> The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA.

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-04T19:09:51Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by <scene name='56/562422/Tata_binding_tata/2'> TBP of the TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. <ref name=Berg/> As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site. <ref name=Berg/>

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. TBP is a 30-kd component of the 700-kd TFIID complex. TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface.

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic_orange/1'>hydrophobic under-surface of the TBP saddle</scene> At the binding site,<scene name='56/567282/Phe/1'>four phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA.

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-04T19:06:38Z

Melissa Kramer:

== Yeast TATA-Box-Binding Protein/TATA-Box Complex ==
<StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1ytb]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

== Overview ==
The 2.5 A crystal structure of a TATA-box complex with yeast TATA-box-binding protein (TBP) is shown at the right (<scene name='56/567282/1ytb_default/1'>1ytb</scene> is a two chain structure with sequence from Saccharomyces cerevisiae that is bound to the TATA-box complex of DNA). <ref name=Kim>PMID:008413604</ref> A key initial step in TATA-box promoters is the recognition by <scene name='56/562422/Tata_binding_tata/2'> TBP of the TATA box.</scene> <ref name=Berg>Berg JM, Tymoczko JL, and Stryer L. Biochemistry. 6th ed. Basingstoke: W.H. Freeman & Co, 2006. 836-37. Print.</ref> TBP initiates strand separation on binding to DNA. As a key factor in the transcription preinitiation complex, TBP helps situate the RNA polymerase II over a gene’s transcription start site.

==Structure==
Its characteristic saddle-shape consists of two similar domains. The saddle-shape of TBP provides docking sites that allow other transcription factors and proteins to bind. TBP and numerous TBP-associated factors interact to make TFIID, a transcription factor that is part of the active RNA polymerase II transcription complex. TBP is a 30-kd component of the 700-kd TFIID complex. TBP-DNA interactions contain many important structural features. One important feature of the TBP is that its long dimension follows the trajectory of the minor groove of the DNA. TBP interacts with the DNA through the concave side of the <scene name='56/567282/Beta_sheets_dna_tbp/1'> β-sheet.</scene> Conserved between the two subdomains are two <scene name='56/567282/Basic_residues_of_tbp/1'>rows of basic residues</scene> that lie along the edges of the protein in proximity to the phosphates in DNA. Down the middle of the groove between the two rows of basic residues lies a band of hydrophobic residues runs down the center of the DNA-binding surface.

==Mechanism for Binding to DNA==
The concave surface of TBP is the site where eight base pairs of the TATA box of DNA binds. On binding, it induces large conformation changes in the bound DNA where it bends the major groove of DNA with unprecedented severity and causes the double helix to become significantly underwound. <ref name=Kim/> The purpose of the conformation changes is to widen the double helix’s minor groove, which allows the DNA to render extensive contact with the antiparallel β strands that are located on the concave side of the TBP. The main types of interactions at this interface are hydrophobic interactions between the minor groove and the entire <scene name='56/567282/Hydrophobic_orange/1'>hydrophobic under-surface of the TBP saddle</scene> At the binding site,<scene name='56/567282/Phe/1'>four phenylalanine residues</scene> intercalate themselves between the TATA box base pairs on the DNA. The resulting severe bend and positive writhe alters the trajectory of the flanking B-form DNA. The <scene name='56/567282/Lys_133_145_151/1'>Lys 133,145,151</scene> are involved in the function of recruiting TFIIA.

</StructureSection>

==Reference==

<references/>

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-03T20:24:39Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-03T20:20:30Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T14:17:46Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T14:14:10Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T14:12:48Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:55:28Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:54:52Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:54:15Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:53:22Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:50:59Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:47:43Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:46:14Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:37:56Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:37:28Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:35:45Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:35:00Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T12:33:04Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T00:23:43Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T00:21:26Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T00:16:32Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T00:06:25Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T00:04:38Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T00:03:52Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-02T00:02:44Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-01T23:51:51Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-01T23:51:25Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-01T23:22:49Z

Melissa Kramer:

SANDBOX YEAST TATA-BOX-BINDING PROTEIN/TATA-BOX COMPLEX

2013-11-01T22:13:35Z

Melissa Kramer: New page: == Yeast TATA-Box-Binding Protein/TATA-Box Complex == <StructureSection load='1ytb' size='350' side='right' caption='Structure of TATA-Box-Binding Protein/TATA-Box Complex (PDB entry [[1yt...

Ann Taylor sandbox 10

2013-10-05T20:41:18Z

Melissa Kramer:

{{STRUCTURE_2ada| PDB=2ada | SCENE= }}

===ADENOSINE DEAMINASE===

Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the <scene name='38/386187/Beta_barrel_active_site/2'>beta-barrel</scene> COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='38/386187/Zinc_cofactor/2'>zinc cofactor</scene>, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue.

The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex.

ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, <scene name='38/386187/Asp295/2'>Asp295</scene>, and <scene name='38/386187/His238/1'>His 238</scene>. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated <scene name='38/386187/Glu217/1'>Glu217</scene> or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.

<references/>

Ann Taylor sandbox 10

2013-10-05T20:35:18Z

Melissa Kramer:

{{STRUCTURE_2ada| PDB=2ada | SCENE= }}

===ADENOSINE DEAMINASE===

Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the <scene name='38/386187/Beta_barrel_active_site/2'>beta barrel</scene> COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='38/386187/Zinc_cofactor/2'>zinc cofactor</scene>, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue.

The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex.

ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, <scene name='38/386187/Asp295/2'>Asp295</scene>, and <scene name='38/386187/His238/1'>His 238</scene>. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated <scene name='38/386187/Glu217/1'>Glu217</scene> or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.

<references/>

Ann Taylor sandbox 10

2013-10-05T20:32:57Z

Melissa Kramer:

{{STRUCTURE_2ada| PDB=2ada | SCENE= }}

===ADENOSINE DEAMINASE===

Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the <scene name='38/386187/Beta_barrel_active_site/2'>beta barrel</scene> COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='38/386187/Zinc_cofactor/1'>zinc cofactor</scene>, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue.

The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex.

ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, <scene name='38/386187/Asp295/2'>Asp295</scene>, and <scene name='38/386187/His238/1'>His 238</scene>. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated <scene name='38/386187/Glu217/1'>Glu217</scene> or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.

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