Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: Specific recognition of a protein-DNA interface

Genes and Development

Volumn 13, Issue 20, 1999, Pages 2650-2657

  Chasman, Daniel ^a,c   Cepek, Karyn ^a,d   Sharp, Phillip A ^a   Pabo, Carl O ^a,b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c Variagenics   (United States)

^d VERTEX PHARMACEUTICALS   (United States)

Author keywords

Crystal structure; Immunoglobulin; OCA B; Oct 1; Octamer; POU domain; Protein DNA complex; Protein DNA interface; Transcription

Indexed keywords

DNA; PEPTIDE; PEPTIDE OCA B; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; B LYMPHOCYTE DIFFERENTIATION; CRYSTAL STRUCTURE; DNA PROTEIN COMPLEX; HYDROGEN BOND; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN PURIFICATION; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; ELECTROSTATICS; HOST CELL FACTOR C1; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OCTAMER TRANSCRIPTION FACTOR-1; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 0033569643     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.13.20.2650     Document Type: Article

References (34)

1. Assa-Munt, N., R.J. Mortishire-Smith, R. Aurora, W. Herr, and P.E. Wright. 1993. The solution structure of the Oct-1 POU-specific domain reveals a striking similarity to the bacteriophage lambda repressor DNA-binding domain. Cell 73: 193-205.
2. Babb, R., M.A. Cleary, and W. Herr. 1997. OCA-B is a functional analog of VP16 but targets a separate surface of the Oct-1 POU domain. Mol. Cell Biol. 17: 7295-7305.
3. Batchelor, A.H., D.E. Piper, F.C. de la Brousse, S.L. McKnight, and C. Wolberger. 1998. The structure of GABPalpha/beta: An ETS domain-ankyrin repeat heterodimer bound to DNA. Science 279: 1037-1041.
4. Brunger, A. 1996. XPLOR, v. 3.851. Yale University, New Haven, CT.
5. Cepek, K.L., D.I. Chasman, and P.A. Sharp. 1996. Sequence-specific DNA binding of the B-cell-specific coactivator OCA-B. Genes & Dev. 10: 2079-2088.
6. Chen, F.E., D.B. Huang, Y.Q. Chen, and G. Ghosh. 1998a. Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature 391: 410-413.
7. Chen, L., J.N. Glover, P.C. Hogan, A. Rao, and S.C. Harrison. 1998b. Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA. Nature 392: 42-48.
8. Collaborative Computational Project Number 4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50: 760-763.
9. Connolly, M.L. 1983. Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709-713.
10. Cowtan, K. 1994. 'dm': An automated procedure for phase improvement by density modification. In Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31: 34-38. Daresbury Laboratory, Warrington, UK.
11. Dekker, N., M. Cox, R. Boelens, C.P. Verrijzer, P.C. van der Vliet, and R. Kaptein. 1993. Solution structure of the POU-specific DNA-binding domain of Oct-1. Nature 362: 852-855.
12. Evans, S. 1993. Setor: Hardware lighted three-dimensional model representations of macromolecules. J. Mol. Graphics 11: 134-138.
13. Ford, E., M. Strubin, and N. Hernandez. 1998. The Oct-1 POU domain activates snRNA gene transcription by contacting a region in the SNAPc largest subunit that bears sequence similarities to the Oct-1 coactivator OBF-1. Genes & Dev. 12: 3528-3540.
14. Gstaiger, M., L. Knoepfel, O. Georgiev, W. Schaffner, and C.M. Hovens. 1995. A B-cell coactivator of octamer-binding transcription factors. Nature 373: 360-362.
15. Gstaiger, M., O. Georgiev, H. van Leeuwen, P. van der Vliet, and W. Schaffner. 1996. The B-cell coactivator Bob1 shows DNA sequence-dependent complex formation with Oct-1/Oct-2 factors, leading to differential promoter activation. EMBO J. 15: 2781-2790.
16. Jacobson, E.M., P. Li, A. Leon-del-Rio, M.G. Rosenfeld, and A.K. Aggarwal. 1997. Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility. Genes & Dev. 11: 198-212.
17. Jones, T. 1992. A set of averaging programs. In Molecular replacement (ed. E. Dodson, S. Cover, and W. Wolf), pp. 91-105. SERC Daresbury Laboratory, Warrington, UK.
18. Jones, T.A., J.-Y. Zou, S.W. Cowan, and M. Kjelgaard. 1991. Improved methods for the building of protein models in electron density maps and the location of errors in these. Acta Crystallogr. A47: 110-119.
19. Kim, U., X.F. Qin, S. Gong, S. Stevens, Y. Luo, M. Nussenzweig, and R.G. Roeder. 1996. The B-cell-specific transcription coactivator OCA-B/OBF-1/Bob-1 is essential for normal production of immunoglobulin isotypes. Nature 383: 542-547.
20. Klemm, J.D., M.A. Rould, R. Aurora, W. Herr, and C.O. Pabo. 1994. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 77: 21-32.
21. La Fortelle, E. and G. Bricogne. 1997. Maximum-likelihood heavy-atom parameter refinement in the MIR and MAD Methods. In Methods in Enzymology, Macromolecular Crystallography (ed. C. W. Carter, Jr. and R. M. Sweet), pp. 472-494. Academic Press, New York, NY.
22. Laskowski, R.A., M.W. MacArthur, D.S. Moss, and J.M. Thornton. 1993. PROCHECK - A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26: 283-291.
23. Li, T., M.R. Stark, A.D. Johnson, and C. Wolberger. 1995. Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science 270: 262-269.
24. Luo, Y. and R.G. Roeder. 1995. Cloning, functional characterization, and mechanism of action of the B-cell-specific transcriptional coactivator OCA-B. Mol. Cell Biol. 15: 4115-4124.
25. Luo, Y., H. Fujii, T. Gerster, and R.G. Roeder. 1992. A novel B-cell-derived coactivator potentiates the activation of immunoglobulin promoters by octamer-binding transcription factors. Cell 71: 231-241.
26. Luo, Y., H. Ge, S. Stevens, H. Xiao, and R.G. Roeder. 1998. Coactivation by OCA-B: definition of critical regions and synergism with general cofactors. Mol. Cell Biol. 18: 3803-3810.
27. Mittal, V., M.A. Cleary, W. Herr, and N. Hernandez. 1996. The Oct-1 POU-specific domain can stimulate small nuclear RNA gene transcription by stabilizing the basal transcription complex SNAPc. Mol. Cell Biol. 16: 1955-1965.
28. Navaza, J. 1994. AMoRe: An automated package for molecular replacement. Acta Crystallogr. A50: 157-163.
29. Otwinowski, Z. and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology, Macromolecular crystallography (ed. C.W. Carter, Jr., and R.M. Sweet), Vol. 276, pp.307-326. Academic Press, New York, NY
30. Read, R.J. 1986. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42: 140-149.
31. Sauter, P. and P. Matthias. 1998. Coactivator OBF-1 makes selective contacts with both the POU-specific domain and the POU homeodomain and acts as a molecular clamp on DNA. Mol. Cell Biol. 18: 7397-7409.
32. Schubart, D.B., A. Rolink, M.H. Kosco-Vilbois, F. Botteri, and P. Matthias. 1996. B-cell-specific coactivator OBF-1/OCA-B/ Bob1 required for immune response and germinal centre formation. Nature 383: 538-542.
33. Strubin, M., J.W. Newell, and P. Matthias. 1995. OBF-1, a novel B cell-specific coactivator that stimulates immunoglobulin promoter activity through association with octamer-binding proteins. Cell 80: 497-506.
34. Tan, S. and T.J. Richmond. 1998. Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 391: 660-666.