A theoretical study of the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II

Science China Chemistry

Volumn 55, Issue 9, 2012, Pages 1887-1894

  Zhang, Yue ^a,b   Salahub, Dennis ^b  

^a SHAANXI NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

Active center; Nucleotidyl transfer reaction; Two metal ion mechanism; Two proton transfer; Yeast RNA polymerase II

Indexed keywords

ACTIVE CENTER; TRANSFER REACTION; TWO-METAL-ION MECHANISM; TWO-PROTON-TRANSFER; YEAST RNA;

CATALYSIS; COMPUTER SIMULATION; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULES; OXYGEN; POLYMERS; QUANTUM THEORY; REACTION KINETICS; YEAST;

RNA;

EID: 84866095413     PISSN: 16747291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11426-012-4708-5     Document Type: Article

References (28)

1. Nudler E. RNA polymerase active center: The molecular engine of transcription. Annu Rev Biochem, 2009, 78: 335-361
2. Svetlov V, Nudler E. Macromolecular micromovements: How RNA polymerase translocates. Curr Opin Struct Biol, 2009, 19: 701-707
3. Brueckner F, Ortiz J, Cramer P. A movie of the RNA polymerase nucleotide addition cycle. Curr Opin Struct Biol, 2009, 19: 294-299
4. Steitz TA. Structural biology: A mechanism for all polymerases. Nature, 1998, 391: 231-232
5. Castro C, Smidansky ED, Arnold JJ, Maksimchuk KR, Moustafa I, Uchida A, Gotte M, Konigsberg W, Cameron CE. Nucleic acid polymerases use a general acid for nucleotidyl transfer. Nat Struct Mol Biol, 2009, 16: 212-218
6. Venkatasubban KS, Schowen RL. The proton inventory technique. Crit Rev Biochem, 1984, 17: 1-44
7. Castro C, Smidansky E, Maksimchuk KR, Arnold JJ, Korneeva VS, Gotte M, Konigsberg W, Cameron CE. Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polyrnerases. Proc Natl Acad Sci USA, 2007, 104: 4267-4272
8. Balbo PB, Bohm A. Proton transfer in the mechanism of polyadenylate polymerase. Biochem J, 2009, 420: 229-238
9. Zhu R, Janetzko F, Zhang Y, van Duin ACT, Goddard WA, Salahub DR. Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations. Theor Chem Acc, 2008, 120: 479-489
10. Florian J, Goodman MF, Warshel A. Computer simulation of the chemical catalysis of DNA polymerases: Discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. J Am Chem Soc, 2003, 125: 8163-8177
11. Bojin MD, Schlick T. A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase beta. J Phys Chem B, 2007, 111: 11244-11252
12. Cukierman S. Et tu, Grotthuss! and other unfinished stories. Biochim Biophy Acta, Bioenerg, 2006, 1757: 876-885
13. Wang LH, Broyde S, Zhang YK. Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: Insights from a study of T7 DNA polymerase. J Mol Biol, 2009, 389: 787-796
14. Wang LH, Yu XY, Hu P, Broyde S, Zhang YK. A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. J Am Chem Soc, 2007, 129: 4731-4737
15. van Duin ACT, Dasgupta S, Lorant F, Goddard WA. ReaxFF: A reactive force field for hydrocarbons. J Phys Chem A, 2001, 105: 9396-9409
16. Zhu R, Salahub DR. Mechanisms of nucleotidyl transfer catalyzed by the yeast RNA polymerase II. In Maroulis G, Simos TE, Eds. Computational Methods in Science and Engineering: Theory and Computation: Old problems and new challenges. Lectures Presented at the International Conference ... Physics. Woodbury, NY: American Institute of Physics Inc. 2007, 963: 104-110
17. Debler EW, Muller R, Hilvert D, Wilson IA. An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket. Proc Natl Acad Sci U S A, 2009, 106: 18539-18544
18. Berdis AJ. Mechanisms of DNA polymerases. Chem Rev, 2009, 109: 2862-2879
19. Muller R, Debler EW, Steinmann M, Seebeck FP, Wilson IA, Hilvert D. Bifunctional catalysis of proton transfer at an antibody active site. J Am Chem Soc, 2007, 129: 460-461
20. Alberts IL, Wang Y, Schlick T. DNA polymerase beta catalysis: Are different mechanisms possible? J Am Chem Soc, 2007, 129: 11100-11110
21. Florian J, Goodman MF, Warshel A. Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases. Proc Natl Acad Sci U S A, 2005, 102: 6819-6824
22. Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis. Cell, 2006, 127: 941-954
23. Wang D, Bushnell DA, Huang XH, Westover KD, Levitt M, Kornberg RD. Structural basis of transcription: Backtracked RNA polymerase II at 3.4 Angstrom resolution. Science, 2009, 324: 1203-1206
24. Liu X, Bushnell DA, Wang D, Calero G, Kornberg RD. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science, 2010, 327: 206-209
25. Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP. Crystal structure of the catalytic core of an RNApolymerase ribozyme. Science, 2009, 326: 1271-1275
26. Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: The biomolecular simulation program. J Comput Chem, 2009, 30: 1545-1614
27. Fiala KA, Suo Z. Mechanism of DNA polymerization catalyzed by Sulfolobus solfataricus P2 DNA polymerase IV. Biochemistry, 2004, 43: 2116-2125
28. Williams AA, Darwanto A, Theruvathu JA, Burdzy A, Neidigh JW, Sowers LC. Impact of sugar pucker on base pair and mispair stability. Biochemistry, 2009, 48: 11994-12004