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(12) Patent Application Publication (10) Pub. No.: US 2003/0232369 A1 Bushnell Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2003/0232369 A1 Bushnell Et Al US 2003O232369A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/0232369 A1 Bushnell et al. (43) Pub. Date: Dec. 18, 2003 (54) MOLECULAR STRUCTURE OF RNA Publication Classification POLYMERASE II (51) Int. Cl." ............................ C12O 1/68; G06F 19/00; (76) Inventors: David A. Bushnell, Menlo Park, CA G01N 33/48; G01N 33/50 (US); Roger D. Kornberg, Atherton, (52) U.S. Cl. ................................................... 435/6; 702/20 CA (US); Patrick Cramer, Munich (DE) (57) ABSTRACT Correspondence Address: Crystals and structures are provided for an eukaryotic RNA BOZICEVIC, FIELD & FRANCIS LLP polymerase, and an elongation complex containing a 200 MIDDLEFIELD RID eukaryotic RNA polymerase. The Structures and structural coordinates are useful in Structural homology deduction, in SUTE 200 developing and Screening agents that affect the activity of MENLO PARK, CA 94025 (US) eukaryotic RNA polymerase, and in designing modified Appl. No.: 10/418,772 forms of eukaryotic RNA polymerase. The structure infor (21) mation may be provided in a computer readable form, e.g. (22) Filed: Apr. 17, 2003 as a database of atomic coordinates, or as a three-dimen Sional model. The Structures are useful, for example, in Related U.S. Application Data modeling interactions of the enzyme with DNA, RNA, transcription factors, nucleotides, etc. The Structures are also (60) Provisional application No. 60/373,486, filed on Apr. used to identify molecules that bind to or otherwise interact 17, 2002. with Structural elements in the polymerase. Rpb1 active site loop Rpb1 (133-c.35 Rpb1 it 3i 1 Patent Application Publication Dec. 18, 2003 Sheet 1 of 26 US 2003/0232369 A1 FIGURE 1 Rpb1 active site loop A. Rpb1 (33-c.35 Rpbit 311 Mr Fourier Patent Application Publication Dec. 18, 2003 Sheet 2 of 26 US 2003/0232369 A1 FIGURE 2 tA . termy". "+ . (-i - - -gs. - t. E . .'; iii w title1 RS: 3. 4...t'w is to textsarawatu - - ... y - 2 : h in i , it i s : 8 , ; c. 2. g . ... FA far Patent Application Publication Dec. 18, 2003. Sheet 3 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003 Sheet 4 of 26 US 2003/0232369 A1 FIGURE 3 s 3. Frase it n n e a. a it was 1 - 1...ft::p. al-A----r: rs. r in . F. kay wa 48 c: Patent Application Publication Dec. 18, 2003. Sheet 5 of 26 US 2003/0232369 A1 FIGURE 3D Exterial 1 & 2 O) (238). 2 75 23-iss's gyat e20 so. QS; : SYs 28 "...Iy \, is SY}S. C- M- is "...(Si) ir is - JC-?yc. si G. - 25, 4. (SS-4s,t jS y) sité (S21 y s \'? 535:5 S N'...f. (53. SS is: t 3.a.)ps. S632.s 3.3%7 Metal A. E. f so. - M afr sial Aof- Kg'isia S. sa lic:30 ... 8 7. switch a pil 3. fiq Hybrid binding . s Patent Application Publication Dec. 18, 2003. Sheet 6 of 26 US 2003/0232369 A1 ·v?gn?H Patent Application Publication Dec. 18, 2003 Sheet 7 of 26 US 2003/0232369 A1 FIGURE 5 Patent Application Publication Dec. 18, 2003. Sheet 8 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003. Sheet 9 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003. Sheet 10 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003. Sheet 11 of 26 US 2003/0232369 A1 **. **. aIppeS% Patent Application Publication Dec. 18, 2003. Sheet 12 of 26 US 2003/0232369 A1 S Patent Application Publication Dec. 18, 2003. Sheet 13 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003. Sheet 14 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003 Sheet 15 of 26 US 2003/0232369 A1 si is 4 c : . it is s is is is ii is . i. s. i & S. i - E - - : . Patent Application Publication Dec. 18, 2003. Sheet 16 of 26 US 2003/0232369 A1 e o Patent Application Publication Dec. 18, 2003. Sheet 17 of 26 US 2003/0232369 A1 FIGURE 15 Sarities E switch 3 Syric 3 switch 2 is is if etplate Patent Application Publication Dec. 18, 2003. Sheet 18 of 26 US 2003/0232369 A1 s s s s f & st'' in a S N\, Patent Application Publication Dec. 18, 2003. Sheet 19 of 26 US 2003/0232369 A1 /|ERH[15)|–| Patent Application Publication Dec. 18, 2003. Sheet 20 of 26 US 2003/0232369 A1 ^^ºeqe!!SqnS(~~~~ ,ellsfiulpu?q effpua?O|-- Patent Application Publication Dec. 18, 2003. Sheet 21 of 26 US 2003/0232369 A1 FIGURE 19 Patent Application Publication Dec. 18, 2003. Sheet 22 of 26 US 2003/0232369 A1 OZEHnºl Patent Application Publication Dec. 18, 2003. Sheet 23 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003. Sheet 24 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003. Sheet 25 of 26 US 2003/0232369 A1 Patent Application Publication Dec. 18, 2003. Sheet 26 of 26 US 2003/0232369 A1 Figure 2. Rpb4 charged EM placement of Rpb 4/7 domain Top US 2003/0232369 A1 Dec. 18, 2003 MOLECULAR STRUCTURE OF RNA activation defect at most promoters tested. These results POLYMERASE II confirm the interaction of Rpb4 and Rpb7 in vivo, and show that the heterodimer also fits the definition of a transcrip BACKGROUND OF THE INVENTION tional “coactivator.” 0001. The control of gene transcription is essential to the 0007. The incredible importance of RNA polymerase in functioning of cellular organisms. By regulating which cellular physiology makes its Structural determination of genes are transcribed and when, the cell is able to respond great interest for development of therapeutic agents, for to Stimuli, proliferate, and differentiate. And when gene molecular design, and for manipulation of gene expression. regulation goes awry, the consequences to the cell, and 0008 Relevant Literature potentially to the organism, can be fatal. 0009 Cramer et al. (2000) Science 288(5466):640-9 dis 0002 The multisubunit enzyme RNA polymerase II (also close the architecture of RNA polymerase II, and a backbone called RNA polymerase b, Rpb, or Pol II) is the central structure. Poglitsch et al. (1999) Cell 98(6):791-8 provide an enzyme of gene expression in eukaryotes. It reads the electron crystal structure of an RNA polymerase II tran sequence of one strand of the DNA double helix (the scription elongation complex. Asturias et al. (1997) J Mol template) and in So doing Synthesizes messenger RNA Biol. 272(4):536-40 reveal two conformations of RNA poly (mRNA), which is then translated into protein. Pol II tran merase II by electron crystallography. Jensen et al. (1998) Scription is the first Step in gene expression and a focal point EMBO J. 17(8):2353-8 disclose the structure of wild-type of cell regulation. It is a target of many Signal transduction yeast RNA polymerase II and location of Rpb4 and Rpb7. Fu pathways, and a molecular Switch for cell differentiation in et al. (1998) J Mol Biol. 280(3):317-22 disclose repeated development. tertiary fold of RNA polymerase II and implications for 0.003 Pol II stands at the center of complex machinery, DNA binding. Gnatt et al. (1997) J Biol Chem. whose composition changes in the course of gene transcrip 272(49):30799-805 disclose the formation and crystalliza tion. This eukaryotic RNA polymerase comprises upwards tion of yeast RNA polymerase II elongation complexes. Fu of a dozen Subunits with a total molecular mass of around et al. (1999) Cell 98(6):799-810 provide a structure of yeast 500 kDa. AS many as six general transcription factors RNA polymerase II at 5 A resolution. assemble with Pol II for promoter recognition and melting. 0010) A review of RNA polymerase II transcription fac A multiprotein Mediator transduces regulatory information tors may be found in Reinberg et al. (1998) Cold Spring from activators and repressors. Additional regulatory pro Harb Symp Quant Biol. 63:83-103. Woychik (1998) Cold teins interact with Pol II during RNA chain elongation, as do Spring HarbSymp Quant Biol. 63:311-7 reviews the func enzymes for RNA capping, splicing, and cleavage/polyade tion of RNA polymerase 11. The mechanism and regulation nylation. of yeast RNA polymerase II transcription is discussed by 0004 Pol II is comprised of 12 subunits, with a total mass Sayre and Kornberg (1993) Cell Mol Biol Res. 39(4):349-54. of greater than 0.5 MD. A backbone model of a 10-subunit 0011 U.S. Pat. No. 6,225,076, Darst et al., discloses a yeast Pol II (lacking two small subunits dispensable for Structure of a prokaryotic RNA polymerase. transcription) was previously obtained by X-ray diffraction and phase determination to approximately 3.5 A resolution SUMMARY OF THE INVENTION (Cramer et al. (2000) Science 288:640). The model revealed 0012 Methods and compositions are provided for mod the general architecture of the enzyme and led to proposals eling the structure of RNA polymerase II, and for identifying for interactions with DNA and RNA in a transcribing molecules that will bind to, and otherwise interact, with complex. functional elements of the polymerase, thereby affecting 0005 RNA polymerase II (pol II) has been isolated in transcription. The methods of the invention entail Structural two forms, a 12-subunit “complete” enzyme and a 10-sub modeling, and the identification and design of molecules unit “core.” The two additional subunits of the complete having a particular structure. The Structural data obtained for enzyme, Rpb4 and Rpb7, form a heterodimer and associate the two forms of RNA polymerase II, for an elongation reversibly with core.
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