RNA Polymerase II

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Yeast RNA Polymerase II complex with RNA (PDB code 1i6h)

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

Brueckner, F. and Cramer, P. Structural Basis of Transcription Inhibition by -amanitin and Implications for RNA Polymerase II Translocation. Nature Structure and Molecular Biology. 2008, 15, 811-818.

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.

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

Hahn, S. Structure and Mechanism of the RNA Polymerase II Transcription Machinery. Nature Structure and Molecular Biology. 2004, 11, 394-403.

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

Nudler, E. RNA Polymerase Active Center: The Molecular Engine of Transcription. Annu. Rev. Biochem. 2009, 78, 335-361.

Orphanides, George, Thierry Lagrange, and Danny Reinberg. The general transcription factors of RNA polymerase II. Genes & development 10.21. 1996. 2657-2683

Shah, N. et. al. Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals. Molecular Cell. 2018, 69, 48-61.

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.

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

Xin, L.; Bushnell, D. A.; and Kornburg, R. D. RNA Polymerase II Transcription: Structure and Mechanism. Biochemica et Biophysica Acta. 2013, 1829, 2-8.

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.

Alpha-aminitin chemical structure image courtesy of https://en.wikipedia.org/wiki/Alpha-Amanitin#/media/File:Alpha-amanitin_structure.png

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]


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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.

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

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