Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes

Structure

Volumn 14, Issue 3, 2006, Pages 555-565

  Lamoureux, Jason S ^a   Glover, J N Mark ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CATION; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; ATOM; DNA BINDING; HYDROGEN BOND; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PROTEIN VARIANT; X RAY CRYSTALLOGRAPHY;

BASE COMPOSITION; BASE PAIRING; BASE SEQUENCE; CONSENSUS SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; PROTEIN CONFORMATION; SACCHAROMYCES CEREVISIAE PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS; VARIATION (GENETICS);

SACCHAROMYCES CEREVISIAE;

EID: 33644847999     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2005.11.017     Document Type: Article

References (31)

1. J. Bravo, Z. Li, N.A. Speck, and A.J. Warren The leukemia-associated AML1 (Runx1)-CBF beta complex functions as a DNA-induced molecular clamp Nat. Struct. Biol. 8 2001 371 378
2. S. Chu, J. DeRisi, M. Eisen, J. Mulholland, D. Botstein, P.O. Brown, and I. Herskowitz The transcriptional program of sporulation in budding yeast Science 282 1998 699 705
3. S. Chu, and I. Herskowitz Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80 Mol. Cell 1 1998 685 696
4. CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
5. W.L. DeLano The PyMOL Molecular Graphics System 2002 DeLano Scientific San Carlos, CA
6. I.M. Fingerman, K. Sutphen, S.P. Montano, M.M. Georgiadis, and A.K. Vershon Characterization of critical interactions between Ndt80 and MSE DNA defining a novel family of Ig-fold transcription factors Nucleic Acids Res. 32 2004 2947 2956
7. S.R. Hepworth, L.K. Ebisuzaki, and J. Segall A 15-base-pair element activates the SPS4 gene midway through sporulation in Saccharomyces cerevisiae Mol. Cell. Biol. 15 1995 3934 3944
8. S.R. Hepworth, H. Friesen, and J. Segall NDT80 and the meiotic recombination checkpoint regulate expression of middle sporulation-specific genes in Saccharomyces cerevisiae Mol. Cell. Biol. 18 1998 5750 5761
9. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr A 47 (Pt. 2) 1991 110 119
10. J.S. Lamoureux, J.T. Maynes, and J.N. Glover Recognition of 5′-YpG-3′ sequences by coupled stacking/hydrogen bonding interactions with amino acid residues J. Mol. Biol. 335 2004 399 408
11. J.S. Lamoureux, D. Stuart, R. Tsang, C. Wu, and J.N. Glover Structure of the sporulation-specific transcription factor Ndt80 bound to DNA EMBO J. 21 2002 5721 5732
12. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
13. X.J. Lu, Z. Shakked, and W.K. Olson A-form conformational motifs in ligand-bound DNA structures J. Mol. Biol. 300 2000 819 840
14. A.P. Mitchell Control of meiotic gene expression in Saccharomyces cerevisiae Microbiol. Rev. 58 1994 56 70
15. S.P. Montano, M.L. Cote, I. Fingerman, M. Pierce, A.K. Vershon, and M.M. Georgiadis Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast Proc. Natl. Acad. Sci. USA 99 2002 14041 14046
16. H.C. Nelson, J.T. Finch, B.F. Luisi, and A. Klug The structure of an oligo(dA).oligo(dT) tract and its biological implications Nature 330 1987 221 226
17. W.K. Olson, A.A. Gorin, X.J. Lu, L.M. Hock, and V.B. Zhurkin DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl. Acad. Sci. USA 95 1998 11163 11168
18. Z. Otwinowski, and W. Minor Processing of X-ray Diffraction Data Collected in Oscillation Mode C.W. Carter Jr. R.M. Sweet Methods in Enzymology 1997 Academic Press New York 307 326
19. N. Ozsarac, M.J. Straffon, H.E. Dalton, and I.W. Dawes Regulation of gene expression during meiosis in Saccharomyces cerevisiae: SPR3 is controlled by both ABFI and a new sporulation control element Mol. Cell. Biol. 17 1997 1152 1159
20. J. Pak, and J. Segall Regulation of the premiddle and middle phases of expression of the NDT80 gene during sporulation of Saccharomyces cerevisiae Mol. Cell. Biol. 22 2002 6417 6429
21. M. Pierce, K.R. Benjamin, S.P. Montano, M.M. Georgiadis, E. Winter, and A.K. Vershon Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression Mol. Cell. Biol. 23 2003 4814 4825
22. M. Pierce, M. Wagner, J. Xie, V. Gailus-Durner, J. Six, A.K. Vershon, and E. Winter Transcriptional regulation of the SMK1 mitogen-activated protein kinase gene during meiotic development in Saccharomyces cerevisiae Mol. Cell. Biol. 18 1998 5970 5980
23. G.G. Prive, U. Heinemann, S. Chandrasegaran, L.S. Kan, M.L. Kopka, and R.E. Dickerson Helix geometry, hydration, and G.A mismatch in a B-DNA decamer Science 238 1987 498 504
24. M. Ptashne A genetic switch: gene control and phage [lamda] 1986 Blackwell Scientific Publications & Cell Press Palo Alto, CA
25. T.H. Tahirov, T. Inoue-Bungo, H. Morii, A. Fujikawa, M. Sasaki, K. Kimura, M. Shiina, K. Sato, T. Kumasaka, and M. Yamamoto Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta Cell 104 2001 755 767
26. K.S. Tung, E.J. Hong, and G.S. Roeder The pachytene checkpoint prevents accumulation and phosphorylation of the meiosis-specific transcription factor Ndt80 Proc. Natl. Acad. Sci. USA 97 2000 12187 12192
27. W. Wang, J.M. Cherry, Y. Nochomovitz, E. Jolly, D. Botstein, and H. Li Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation Proc. Natl. Acad. Sci. USA 102 2005 1998 2003
28. J. Xie, M. Pierce, V. Gailus-Durner, M. Wagner, E. Winter, and A.K. Vershon Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae EMBO J. 18 1999 6448 6454
29. L. Xu, M. Ajimura, R. Padmore, C. Klein, and N. Kleckner NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae Mol. Cell. Biol. 15 1995 6572 6581
30. L. Xu, B.M. Weiner, and N. Kleckner Meiotic cells monitor the status of the interhomolog recombination complex Genes Dev. 11 1997 106 118
31. C. Yoon, G.G. Prive, D.S. Goodsell, and R.E. Dickerson Structure of an alternating-B DNA helix and its relationship to A-tract DNA Proc. Natl. Acad. Sci. USA 85 1988 6332 6336