Structure of the conserved transcriptional repressor enhancer of rudimentary homolog

Biochemistry

Volumn 44, Issue 13, 2005, Pages 5017-5023

  Wan, Cheng ^a   Tempel, Wolfram ^b   Liu, Zhi Jie ^b   Wang, Bi Cheng ^b   Rose, Robert B ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b University of Georgia ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; HYDROPHOBICITY; PLANTS (BOTANY); PROTEINS; PROTOZOA; STRUCTURE (COMPOSITION);

CELL CYCLE; PHOSPHORYLATION; PYRIMIDINE; TRANSCRIPTIONAL COREGULATORS;

BIOCHEMISTRY;

DIMER; NUCLEAR FACTOR I;

ARTICLE; BETA SHEET; CELL CYCLE; CRYSTAL STRUCTURE; DIMERIZATION; ERH GENE; GENETIC TRANSCRIPTION; HYDROPHOBICITY; NONHUMAN; PARALOGY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PYRIMIDINE SYNTHESIS; REPRESSOR GENE;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CELL CYCLE PROTEINS; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ELECTROSTATICS; EVOLUTION, MOLECULAR; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS;

EUKARYOTA; PROTOZOA;

EID: 16344390212     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047785w     Document Type: Article

References (41)

1. Pogge von Strandmann, E., Senkel, S., and Ryffel, G. U. (2001) erh (enhancer of rudimentary homologue), a conserved factor identical between frog and human, is a transcriptional repressor, Biol. Chem. 382, 1379-85.
2. Gelsthorpe, M., Pulumati, M., McCallum, C., Dang-Vu, K., and Tsubota, S. I. (1997) The putative cell cycle gene, enhancer of rudimentary, encodes a highly conserved protein found in plants and animals, Gene 186, 189-95.
3. Isomura, M., Okui, K., Fujiwara, T., Shin, S., and Nakamura, Y. (1996) Cloning and mapping of a novel human cDNA homologous to DROER, the enhancer of the Drosophila melanogaster rudimentary gene, Genomics 32, 125-7.
4. Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., Cooke, M. P., Walker, J. R., and Hogenesch, J. B. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes, Proc. Natl. Acad. Sci. U.S.A. 101, 6062-7.
5. Wojcik, E., Murphy, A. M., Fares, H., Dang-Vu, K., and Tsubota, S. I. (1994) Enhancer of rudimentary p1, e(r)p1, a highly conserved enhancer of the rudimentary gene, Genetics 138, 1163-70.
6. Jancarik, J., and Kim, S. H. (1991) Sparse matrix sampling: a screening method for crystallization of proteins, J. Appl. Crystallogr. 24, 409-11.
7. Holton, J., and Alber, T. (2004) Automated protein crystal structure determination using ELVES, Proc. Natl. Acad. Sci. U.S.A. 101, 1537-42.
8. Leslie, A., Brick, P., and Wonacott, A. (1986) Daresbury Lab. Information Quart. Protein Crystallogr. 18, 33-39.
9. Collaborative Computation Project (1994) The CCP4 suite: programs for protein crystallography, Acta Crystallogr. D50, 760-3.
10. Evans, P. (1993) Proceedings of CCP4 Study Weekend on Data Collection & Processing, pp 114-122, CLRC Daresbury Laboratory, http://www.ccp4.ac.uk/ courses/procs.html.
11. French, G., and Wilson, K. (1978) On the treatment of negative intensity observations, Acta Crystallogr. A34, 517.
12. Wang, B. C. (1985) Resolution of phase ambiguity in macromolecular crystallography, Methods Enzymol. 115, 90-112.
13. Terwilliger, T. C., and Berendzen, J. (1999) Automated MAD and MIR structure solution, Acta Crystallogr., Sect. D 55 (Pt 4), 849-61.
14. Terwilliger, T. C. (2002) Automated structure solution, density modification, and model building, Acta Crystallogr., Sect. D 58, 1937-40.
15. Cowtan, K. D., and Zhang, K. Y. (1999) Density modification for macromolecular phase improvement, Prog. Biophys. Mol. Biol. 72, 245-70.
16. Perrakis, A., Morris, R., and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement, Nat. Struct. Biol. 6, 458-63.
17. McRee, D. E. (1999) XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density, J. Struct. Biol. 125, 156-65.
18. Brunger, A., Adams, P., Clore, G., Delano, W., Gros, P., Grosse-Kunstleve, R., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N., Read, R., Rice, L., Simonson, T., and Warren, G. (1998) Crystallography and NMR system (CNS): a new software system for macromolecular structure determination, Acta Crystallogr., Sect. D 54, 905-21.
19. Potterton, E., Briggs, P., Turkenburg, M., and Dodson, E. (2003) A graphical user interface to the CCP4 program suite, Acta Crystallogr., Sect. D 59, 1131-7.
20. Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S., and Dodson, E. J. (1999) Efficient anisotropic refinement of macromolecular structures using FFT, Acta Crystallogr. Sect. D 55 (Pt 1), 247-55.
21. Jones, T., Zhou, J., Cowan, S., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr., Sect. A 47, 110-9.
22. Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-402.
23. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice, Nucleic Acids Res. 22, 4673-80.
24. Matthews, B. W. (1968) Solvent content of protein crystals, J. Mol. Biol. 33, 491-7.
25. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol. 247, 536-40.
26. Jones, S., and Thornton, J. M. (1995) Protein-protein interactions: a review of protein dimer structures, Prog. Biophys. Mol. Biol. 63, 31-65.
27. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank, Nucleic Acids Res. 28, 235-42.
28. Ginalski, K., Elofsson, A., Fischer, D., and Rychlewski, L. (2003) 3D-Jury: a simple approach to improve protein structure predictions, Bioinformatics 19, 1015-8.
29. Kelley, L. A., MacCallum, R. M., and Sternberg, M. J. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM, J. Mol. Biol. 299, 499-520.
30. Jones, D. T. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences, J. Mol. Biol. 287, 797-815.
31. McGuffin, L. J., and Jones, D. T. (2003) Improvement of the GenTHREADER method for genomic fold recognition, Bioinformatics 19, 874-81.
32. Wallner, B., Fang, H., and Elofsson, A. (2003) Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller, Proteins 53 Suppl 6, 534-41.
33. Holm, L., and Sander, C. (1995) Dali: a network tool for protein structure comparison, Trends Biochem. Sci. 20, 478-80.
34. Gibrat, J. F., Madej, T., and Bryant, S. H. (1996) Surprising similarities in structure comparison, Curr. Opin. Struct. Biol. 6, 377-85.
35. Gilbert, D., Westhead, D., Nagano, N., and Thornton, J. (1999) Motif-based searching in TOPS protein topology databases, Bioinformatics 15, 317-26.
36. Shindyalov, I. N., and Bourne, P. E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng. 11, 739-47.
37. Rose, R. B., Bayle, J. H., Endrizzi, J. A., Cronk, J. D., Crabtree, G. R., and Alber, T. (2000) Structural basis of dimerization, coactivator recognition, and MODY3 mutations in HNF-1alpha, Nat. Struct. Biol. 7, 744-8.
38. Brownlie, P., Ceska, T., Lamers, M., Romier, C., Stier, G., Teo, H., and Suck, D. (1997) The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control, Structure 5, 509-20.
39. Andrew, C. D., Warwicker, J., Jones, G. R., and Doig, A. J. (2002) Effect of phosphorylation on α-helix stability as a function of position, Biochemistry 41, 1897-905.
40. Blom, N., Gammeltoft, S., and Brunak, S. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites, J. Mol. Biol. 294, 1351-62.
41. Beitz, E. (2000) TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e, Bioinformatics 16, 135-9.