RNA Polymerase II

RNAP II

spinqualitylabelsall models RNA Polymerase II Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Introduction Titus wrote this The cookie monster is now the veggie monster. Structural Components Like in much of biochemistry, the structure of RNAP II gives insights into its function. This is an image with all of the following discussed structures within one image. 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. Other components of RNA pol II include the following: 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 bridge is an Rpb1 segment that translocates the DNA-RNA complex at the end of each cycle of catalysis. Magnesium is located within the active site and functions as the catalyst. Mechanism of Action 1wcm TextToBeDisplayed 1i6h TextToBeDisplayed Alpha Amanitin 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. General Transcription Factors 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. Process of PIC formation: 1. TFIID contains a subunit named the TATA-binding protein (TBP), which recognizes and binds to the TATA box on the DNA promoter. 2. TFIIB and TFIIA and interact with TBP and are recruted to the promoter. 3. TFIIF binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly. 4. TFIIE and TFIIH are sequentually recruited which completes the PIC. 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.

References

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

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

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.

He, Yuan, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533.7603. 2016.

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.

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.

Notes

From structural components:

Structural overview: [PDB: 5VVR: with highlighted sections mentioned below]

Bridge: Depicted: [PDB: 1I6H: 810-845.a]

Wall: Depicted: [PDB: 1R5U: 853-919.b; 933-972.b]

Clamp: Depicted: [PDB: 1R5U: 3-345.a; 1395-1435.a; 1158-1124.b]

Rudder: Depicted: [PDB: 5VVR: 306-321.a]

Content Donators

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.

Proteopedia Page Contributors and Editors (what is this?)

Abraham Kiesel, Titus Edwards, James Daniel Andry, Michal Harel, Wally Novak, Karsten Theis