https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Titus+EdwardsProteopedia - User contributions [en]2026-09-13T09:29:41ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122649RNA Polymerase II2019-12-08T01:28:51Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/3'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/3'>PIC</scene>. <br />
<br />
<br />
<br />
Once the <scene name='82/824648/Pic/3'>PIC</scene> is formed, <scene name='82/824648/Rnap_ii/1'>RNAP II</scene> initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122648RNA Polymerase II2019-12-08T01:28:20Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/3'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/3'>PIC</scene>. <br />
<br />
<br />
<br />
Once the <scene name='82/824648/Pic/3'>PIC</scene> is formed, <scene name='82/824648/Rnap_ii/1'>RNAP II</scene> initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122646RNA Polymerase II2019-12-08T01:19:28Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/3'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/3'>PIC</scene>. <br />
<br />
<br />
<br />
Once the <scene name='82/824648/Pic/3'>PIC</scene> is formed, <scene name='82/824648/Rnap_ii/1'>RNAP II</scene> initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122645RNA Polymerase II2019-12-08T01:12:50Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/2'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/2'>PIC</scene>. <br />
<br />
<br />
<br />
Once the <scene name='82/824648/Pic/2'>PIC</scene> is formed, <scene name='82/824648/Rnap_ii/1'>RNAP II</scene> initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122644RNA Polymerase II2019-12-08T01:10:25Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to <scene name='82/824648/Rnap_ii/1'>RNAP II</scene> and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/2'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/2'>PIC</scene>. <br />
<br />
<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122643RNA Polymerase II2019-12-08T00:53:01Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/2'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122642RNA Polymerase II2019-12-08T00:52:00Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/4'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/2'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122640RNA Polymerase II2019-12-08T00:48:09Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/4'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/2'>TFIIE</scene> and <scene name='82/824648/Tfiih/2'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122639RNA Polymerase II2019-12-08T00:32:01Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/2'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122633RNA Polymerase II2019-12-08T00:19:29Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II transcription process.]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. There are three RNA polymerase enzymes found in eukaryotic nuclei but RNAP II is the most studied. RNAP II is a 550 kDa multi-protein complex that includes 12 subunits. Several transcription factors are used to bind promoters upstream of the start site and are necessary for joining RNAP II and DNA. Bound RNAP II transcribes DNA into a strand of messenger RNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stand transports genetic information from DNA to the ribosome, where it is used to specify the amino acid sequence for the production of proteins. <br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122628RNA Polymerase II2019-12-08T00:06:44Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| RNAP II (Blue), DNA (Red), RNA (Green).]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122627RNA Polymerase II2019-12-08T00:05:40Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
<br />
[[ Image:Label RNA pol II (1).png|150px|right|thumb| Functioning RNAP II (Blue) bound to DNA (Red), producing a newly transcribed strand of RNA (Green).]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122625RNA Polymerase II2019-12-08T00:04:52Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
<br />
[[ Image:Label RNA pol II (1).png|200px|right|thumb| Functioning RNAP II (Blue) bound to DNA (Red), producing a newly transcribed strand of RNA (Green).]]<br />
<br />
<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122623RNA Polymerase II2019-12-08T00:04:14Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
<br />
[[ Image:Label RNA pol II (1).png|100px|left|thumb| Functioning RNAP II (Blue) bound to DNA (Red), producing a newly transcribed strand of RNA (Green).]]<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122622RNA Polymerase II2019-12-08T00:03:55Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
<br />
[[ Image:Label RNA pol II (1).png|250px|left|thumb| Functioning RNAP II (Blue) bound to DNA (Red), producing a newly transcribed strand of RNA (Green).]]<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=File:Label_RNA_pol_II_(1).png&diff=3122621File:Label RNA pol II (1).png2019-12-07T23:59:31Z<p>Titus Edwards: Functioning RNAP II (Blue) bound to DNA (Red), producing a newly transcribed strand of RNA (Green).</p>
<hr />
<div>== Summary ==<br />
Functioning RNAP II (Blue) bound to DNA (Red), producing a newly transcribed strand of RNA (Green).<br />
== Licensing ==<br />
{{subst:Non-commercial from license selector}}</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122619RNA Polymerase II2019-12-07T23:52:02Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122618RNA Polymerase II2019-12-07T23:51:22Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
<br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122617RNA Polymerase II2019-12-07T23:41:09Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122616RNA Polymerase II2019-12-07T23:38:19Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA.Brief description of mRNA. Size and composition???<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122614RNA Polymerase II2019-12-07T23:33:01Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA. Messenger RNA (mRNA) is a single stranded RNA molecule that is complementary to the template strand of DNA. The mRNA stands transport genetic information from DNA to the ribosome, where they are used to specify the amino acid sequence for the production of proteins. RNAP II is a 550 kDa complex that includes 12 subunits.<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122606RNA Polymerase II2019-12-07T22:27:30Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA.Brief description of mRNA. Size and composition???<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/2'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/3'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3122605RNA Polymerase II2019-12-07T22:01:53Z<p>Titus Edwards: </p>
<hr />
<div><StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, and it therefore is responsible for the synthesis of mRNA.Brief description of mRNA. Size and composition???<br />
== Structural Components ==<br />
<br />
This section will briefly discuss the chief structural components involved in the mechanism. <br />
<br />
<br />
[[ Image:RnapII struct features.jpg|300px|left|thumb| The clamp (magenta), wall (navy blue), rudder (red), bridge (orange), RNA (light blue), and DNA (blue) are depicted. See below for PDB's and residue numbers.]]<br />
<br />
To begin, the <scene name='82/824648/Clamp/5'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/2'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/3'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/6'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/3'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>active site apo structure</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>elongation complex</scene><br />
<br />
== α-Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover. <br />
[[Image:Alpha-amanitin structure (1).png|300px|right|thumb| The chemical structure of α-amanitin.]]<br />
<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/1'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/1'>PIC</scene>. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the <scene name='82/824648/Pic/1'>PIC</scene> is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Gnatt, A. L.; Cramer, P; Fu, J.; Bushnell, D. A.; and Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 2001, 292, 1876-1882 1i6h<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Xu, J.; Lahiri, I.; Wang, W.; Wier, A.; Cianfrocco, M. A.; Chong, J.; Hare, A. A.; Dervan, P. B.; DiMaio, F.; Leschziner, A. E.; Wang, D. Structural Basis for the Initiation of Eukaryotic Transcription-coupled DNA Repair. Nature. 2017. 551, 653-657 5vvr<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093050RNA Polymerase II2019-10-08T13:23:38Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, therefore it is responsible for the synthesis of mRNA.Brief description of mRNA<br />
== Structural Components ==<br />
<br />
Like in much of biochemistry, the structure of RNAP II gives insights into its function. <br />
<br />
This is an image with all of the following discussed structures within one image.<br />
<br />
<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/1'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
PIC NON-TRANSPARENT COMPLEX<br />
FIGURE CAPTIONS-PDB AND COLOR<br />
CENTERING F<br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093049RNA Polymerase II2019-10-08T13:21:56Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Introduction ==<br />
RNA polymerase II (RNAP II) is an enzyme that transcribes protein-encoding genes, therefore it is responsible for the synthesis of mRNA.<br />
== Structural Components ==<br />
<br />
Like in much of biochemistry, the structure of RNAP II gives insights into its function. <br />
<br />
This is an image with all of the following discussed structures within one image.<br />
<br />
<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/1'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093048RNA Polymerase II2019-10-08T13:17:59Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Introduction ==<br />
Titus wrote this<br />
<br />
The cookie monster is now the veggie monster. <br />
<br />
== Structural Components ==<br />
<br />
Like in much of biochemistry, the structure of RNAP II gives insights into its function. <br />
<br />
This is an image with all of the following discussed structures within one image.<br />
<br />
<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/1'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093047RNA Polymerase II2019-10-08T13:13:41Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Introduction ==<br />
Titus wrote this<br />
<br />
The cookie monster is now the veggie monster. <br />
<br />
== Structural Components ==<br />
<br />
Like in much of biochemistry, the structure of RNAP II gives insights into its function. <br />
<br />
This is an image with all of the following discussed structures within one image.<br />
<br />
<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiib/1'>TFIIB</scene> and <scene name='82/824648/Tfiia/1'>TFIIA</scene> and interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while <scene name='82/824648/Tfiib/1'>TFIIB</scene> helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093044RNA Polymerase II2019-10-08T12:39:14Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Introduction ==<br />
Titus wrote this<br />
<br />
The cookie monster is now the veggie monster. <br />
<br />
== Structural Components ==<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiia/1'>TFIIA</scene> and <scene name='82/824648/Tfiib/1'>TFIIB</scene> interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
<br />
<br />
== Notes ==<br />
From structural components:<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093043RNA Polymerase II2019-10-08T12:17:28Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Introduction ==<br />
Titus wrote this<br />
<br />
The cookie monster is now the veggie monster. <br />
<br />
== Structural Components ==<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiia/1'>TFIIA</scene> and <scene name='82/824648/Tfiib/1'>TFIIB</scene> interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
== Notes ==<br />
From structural components:<br />
<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093039RNA Polymerase II2019-10-08T11:47:58Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Structural Components ==<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiia/1'>TFIIA</scene> and <scene name='82/824648/Tfiib/1'>TFIIB</scene> interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
== Notes ==<br />
From structural components:<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093038RNA Polymerase II2019-10-08T11:47:20Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Structural Components ==<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter.<br />
<br />
2. <scene name='82/824648/Tfiia/1'>TFIIA</scene> and <scene name='82/824648/Tfiib/1'>TFIIB</scene> interact with TBP and are recruted to the promoter.<br />
<br />
3. <scene name='82/824648/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. <br />
<br />
4. <scene name='82/824648/Tfiie/1'>TFIIE</scene> and <scene name='82/824648/Tfiih/1'>TFIIH</scene> are sequentually recruited which completes the PIC. <br />
<br />
Once the PIC is formed, RNAP II initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation. <br />
<br />
<br />
<scene name='82/824648/Tfiid-tbp/1'>TFIID/TBP</scene> <br />
<br />
<scene name='82/824648/Tfiib/1'>TFIIB</scene><br />
<br />
<scene name='82/824648/Tfiia/1'>TFIIA</scene><br />
<br />
<scene name='82/824648/Tfiif/1'>TFIIF</scene><br />
<br />
<scene name='82/824648/Tfiie/1'>TFIIE</scene><br />
<br />
<scene name='82/824648/Tfiih/1'>TFIIH</scene><br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406.<br />
== Notes ==<br />
From structural components:<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093037RNA Polymerase II2019-10-08T11:19:27Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Structural Components ==<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA binding protein (TBP), which recognizes and binds to the TATA box on the dna promoter<br />
<br />
<scene name='82/824648/Tfiid-tbp/1'>TFIID/TBP</scene><br />
<br />
<scene name='82/824648/Tfiib/1'>TFIIB</scene><br />
<br />
<scene name='82/824648/Tfiia/1'>TFIIA</scene><br />
<br />
<scene name='82/824648/Tfiif/1'>TFIIF</scene><br />
<br />
<scene name='82/824648/Tfiie/1'>TFIIE</scene><br />
<br />
<scene name='82/824648/Tfiih/1'>TFIIH</scene><br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406. https://doi.org/10.1038/s41594-019-0220-3<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
<br />
== Notes ==<br />
From structural components:<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3093036RNA Polymerase II2019-10-08T11:18:26Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II''><br />
<br />
== Structural Components ==<br />
The <scene name='82/824648/Clamp/2'>clamp</scene> swings to trap the DNA in the cleft. Further along, the <scene name='82/824648/Wall/1'>wall</scene> sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the <scene name='82/824648/Rudder/1'>rudder</scene> separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
== Mechanism of Action ==<br />
<br />
1wcm <scene name='82/824544/Active_site_1/1'>TextToBeDisplayed</scene><br />
1i6h <scene name='82/824648/Active_site_2/1'>TextToBeDisplayed</scene><br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclic octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors (GTFs). These GTFs are all named similarly and begin with TF, for transcription factor, followed by the Roman numeral II since they are involved in transcription by RNAP II. The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is called the preinitiation complex (PIC). The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.<br />
<br />
Process of PIC formation:<br />
<br />
1. <scene name='82/824648/Tfiid-tbp/1'>TFIID</scene> contains a subunit named the TATA binding protein (TBP), which recognizes and binds to the TATA box on the dna promoter<br />
<br />
<scene name='82/824648/Tfiid-tbp/1'>TFIID/TBP</scene><br />
<br />
<scene name='82/824648/Tfiib/1'>TFIIB</scene><br />
<br />
<scene name='82/824648/Tfiia/1'>TFIIA</scene><br />
<br />
<scene name='82/824648/Tfiif/1'>TFIIF</scene><br />
<br />
<scene name='82/824648/Tfiie/1'>TFIIE</scene><br />
<br />
<scene name='82/824648/Tfiih/1'>TFIIH</scene><br />
<br />
Yan, C., Dodd, T., He, Y., Tainer, J. A., Tsutakawa, S. E., & Ivanov, I. (2019). Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural and Molecular Biology, 26(6), 397-406. https://doi.org/10.1038/s41594-019-0220-3<br />
<br />
</StructureSection><br />
== References ==<br />
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988<br />
<br />
Cramer, P.; Bushnell, D. A.; Kornberg, R. D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 2001, 292, 1863-1876<br />
<br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000, 122, 10033-10046.<br />
<br />
<br />
== Notes ==<br />
From structural components:<br />
Bridge: Depicted: [PDB: 1I6H: 810-845.a]<br />
Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]<br />
Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]<br />
Rudder: Depicted: [PDB: 5VVR: 306-321.a]<br />
<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3088614RNA Polymerase II2019-10-01T20:14:36Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II' scene=''><br />
This is a default text for your page '''RNA Polymerase II'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
<br />
<br />
== Overview ==<br />
RNA polymerase (RNAP) II<br />
<br />
The <scene name='82/824541/Bridge/1'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis.<br />
<br />
== Structural Components ==<br />
The clamp swings to trap the DNA in the cleft. Further along, the wall sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the rudder separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
== Mechanism of Action ==<br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclinc octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<scene name='82/824648/Tfiid-tbp/1'>TFIID/TBP</scene><br />
<br />
<scene name='82/824648/Tfiib/1'>TFIIB</scene><br />
<br />
<scene name='82/824648/Tfiia/1'>TFIIA</scene><br />
<br />
<scene name='82/824648/Tfiif/1'>TFIIF</scene><br />
<br />
<scene name='82/824648/Tfiie/1'>TFIIE</scene><br />
<br />
<scene name='82/824648/Tfiih/1'>TFIIH</scene><br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Components, Alpha Amanitin, <br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3088606RNA Polymerase II2019-10-01T13:27:52Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II' scene=''><br />
This is a default text for your page '''RNA Polymerase II'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
<br />
<br />
== Overview ==<br />
RNA polymerase (RNAP) II<br />
<br />
The <scene name='82/824541/Bridge/1'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis.<br />
<br />
== Structural Components ==<br />
The clamp swings to trap the DNA in the cleft. Further along, the wall sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the rudder separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
== Mechanism of Action ==<br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclinc octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<scene name='82/824648/Tfiid-tbp/1'>TFIID/TBP</scene><br />
<scene name='82/824648/Tfiib/1'>TFIIB</scene><br />
<scene name='82/824648/Tfiia/1'>TFIIA</scene><br />
TFIIF<br />
TFIIE<br />
TFIIH<br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Components, Alpha Amanitin, <br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3088605RNA Polymerase II2019-10-01T13:15:30Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1i6h' size='340' side='right' caption='RNA Polymerase II' scene=''><br />
This is a default text for your page '''RNA Polymerase II'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
<br />
<br />
== Overview ==<br />
RNA polymerase (RNAP) II<br />
<br />
The <scene name='82/824541/Bridge/1'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis.<br />
<br />
== Structural Components ==<br />
The clamp swings to trap the DNA in the cleft. Further along, the wall sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the rudder separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824648/Bridge/4'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis. <scene name='82/824648/Magnesium/1'>Magnesium</scene> is located within the active site and functions as the catalyst. <br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
== Mechanism of Action ==<br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclinc octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<scene name='82/824648/Tfiid-tbp/1'>TFIID/TBP</scene><br />
<scene name='82/824648/Tfiib/1'>TFIIB</scene><br />
TFIIA<br />
TFIIF<br />
TFIIE<br />
TFIIH<br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Components, Alpha Amanitin, <br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=RNA_Polymerase_II&diff=3088597RNA Polymerase II2019-09-30T23:56:21Z<p>Titus Edwards: </p>
<hr />
<div>== RNAP II ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''RNA Polymerase II'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Overview ==<br />
RNA polymerase (RNAP) II<br />
<br />
The <scene name='82/824541/Bridge/1'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis.<br />
<br />
== Structural Components ==<br />
The clamp swings to trap the DNA in the cleft. Further along, the wall sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the rudder separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II. <br />
<br />
Other components of RNA pol II include the following:<br />
The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The <scene name='82/824541/Bridge/1'>bridge</scene> is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis.<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
== Mechanism of Action ==<br />
<br />
== Alpha Amanitin ==<br />
α-Amanitin is a bicyclinc octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.<br />
<br />
== Modifications ==<br />
<br />
== General Transcription Factors ==<br />
<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
Components, Alpha Amanitin, <br />
Uzman, A.; Voet, D. Student companion Fundamentals of biochemistry: life at the molecular level, 4th ed., Donald Voet, Judith G. Voet, Charlotte W. Pratt; John Wiley & amp; Sons, 2012.<br />
<br />
== Content Donators ==<br />
<br />
This page was created as a final project for the Advanced Biochemistry course at Wabash College during the Fall of 2019. This page was reviewed by Dr. Wally Novak of Wabash College.</div>Titus Edwardshttps://proteopedia.org/index.php?title=User:Titus_Edwards&diff=3088539User:Titus Edwards2019-09-26T11:30:10Z<p>Titus Edwards: </p>
<hr />
<div>* Full Real Name: Titus Edwards<br />
<br />
* Position: Student<br />
<br />
* Institution (NO ABBREVIATIONS): Wabash College<br />
<br />
* City, State/Province, Country: Crawfordsville, Indiana, United States <br />
<br />
* Field of Expertise or Study: Biochemistry<br />
*[[User:Titus Edwards/Sandbox RNAPOL2]]<br />
<Structure load='5FUR' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><br />
<br />
The Transcription Initiation Factor IIA (<scene name='82/824537/Tfiia/1'>TFIIA</scene>) is super cool when colored blue.</div>Titus Edwardshttps://proteopedia.org/index.php?title=User:Titus_Edwards&diff=3088538User:Titus Edwards2019-09-26T11:15:29Z<p>Titus Edwards: </p>
<hr />
<div>* Full Real Name: Titus Edwards<br />
<br />
* Position: Student<br />
<br />
* Institution (NO ABBREVIATIONS): Wabash College<br />
<br />
* City, State/Province, Country: Crawfordsville, Indiana, United States <br />
<br />
* Field of Expertise or Study: Biochemistry<br />
*[[User:Titus Edwards/Sandbox RNAPOL2]]<br />
<Structure load='5FUR' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /></div>Titus Edwardshttps://proteopedia.org/index.php?title=File:2o5iTE.pdb&diff=3088220File:2o5iTE.pdb2019-09-12T13:16:52Z<p>Titus Edwards: </p>
<hr />
<div></div>Titus Edwardshttps://proteopedia.org/index.php?title=User:Titus_Edwards/Sandbox_RNAPOL2&diff=3088218User:Titus Edwards/Sandbox RNAPOL22019-09-12T13:01:37Z<p>Titus Edwards: </p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='2o5i' size='340' side='right' caption='RNA POL Elongation Complex' scene=''><br />
This is a default text for your page '''Titus Edwards/Sandbox RNAPOL2'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
Show <scene name='82/824543/Tacrine/4'>tacrine</scene><br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Titus Edwardshttps://proteopedia.org/index.php?title=User:Titus_Edwards/Sandbox_RNAPOL2&diff=3088214User:Titus Edwards/Sandbox RNAPOL22019-09-12T12:57:29Z<p>Titus Edwards: </p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='2o5i' size='340' side='right' caption='RNA POL Elongation Complex' scene=''><br />
This is a default text for your page '''Titus Edwards/Sandbox RNAPOL2'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<scene name='82/824543/Tacrine/1'>See tacrine</scene><br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Titus Edwardshttps://proteopedia.org/index.php?title=User:Titus_Edwards/Sandbox_RNAPOL2&diff=3088211User:Titus Edwards/Sandbox RNAPOL22019-09-12T12:36:39Z<p>Titus Edwards: </p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='2o5i' size='340' side='right' caption='RNA POL Elongation Complex' scene=''><br />
This is a default text for your page '''Titus Edwards/Sandbox RNAPOL2'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
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</StructureSection><br />
== References ==<br />
<references/></div>Titus Edwardshttps://proteopedia.org/index.php?title=User:Titus_Edwards/Sandbox_RNAPOL2&diff=3088209User:Titus Edwards/Sandbox RNAPOL22019-09-12T12:35:59Z<p>Titus Edwards: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='2o5i' size='340' side='right' caption='Elongation Complex' scene=''> This is a default text for your page '...</p>
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<div>==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='2o5i' size='340' side='right' caption='Elongation Complex' scene=''><br />
This is a default text for your page '''Titus Edwards/Sandbox RNAPOL2'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
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== Function ==<br />
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== Disease ==<br />
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== Relevance ==<br />
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== Structural highlights ==<br />
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
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</StructureSection><br />
== References ==<br />
<references/></div>Titus Edwardshttps://proteopedia.org/index.php?title=User:Titus_Edwards&diff=3088204User:Titus Edwards2019-09-12T12:32:56Z<p>Titus Edwards: </p>
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<div>* Full Real Name: Titus Edwards<br />
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* Position: Student<br />
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* Institution (NO ABBREVIATIONS): Wabash College<br />
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* City, State/Province, Country: Crawfordsville, Indiana, United States <br />
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* Field of Expertise or Study: Biochemistry<br />
*[[User:Titus Edwards/Sandbox RNAPOL2]]</div>Titus Edwards