The DOI matches its Crossref record; 71 of the 71 references it cites were found in a registry or an index.
Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding
Open accessAbstract
Pax6, a transcription factor containing the bipartite paired DNA-binding domain, has critical roles in development of the eye, nose, pancreas, and central nervous system. The 2.5 A structure of the human Pax6 paired domain with its optimal 26-bp site reveals extensive DNA contacts from the amino-terminal subdomain, the linker region, and the carboxy-terminal subdomain. The Pax6 structure not only confirms the docking arrangement of the amino-terminal subdomain as seen in cocrystals of the Drosophila Prd Pax protein, but also reveals some interesting differences in this region and helps explain the sequence specificity of paired domain-DNA recognition. In addition, this structure gives the first detailed information about how the paired linker region and carboxy-terminal subdomain contact DNA. The extended linker makes minor groove contacts over an 8-bp region, and the carboxy-terminal helix-turn-helix unit makes base contacts in the major groove. The structure and docking arrangement of the carboxy-terminal subdomain of Pax6 is remarkably similar to that of the amino-terminal subdomain, and there is an approximate twofold symmetry axis relating the polypeptide backbones of these two helix-turn-helix units. Our structure of the Pax6 paired domain-DNA complex provides a framework for understanding paired domain-DNA interactions, for analyzing mutations that map in the linker and carboxy-terminal regions of the paired domain, and for modeling protein-protein interactions of the Pax family proteins.
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[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475
The CCP4 suite: programs for protein crystallography
Collaborative Computational Project, N. 4. (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994003112 · Cited by 17,270
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
Brünger, A. T. (1992) · Nature · doi:10.1038/355472a0 · Cited by 3,873
Accurate bond and angle parameters for X-ray protein structure refinement
Engh, R. A., & Huber, R. (1991) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767391001071 · Cited by 2,489
Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 Å
Pavletich, N. P., & Pabo, C. O. (1991) · Science · doi:10.1126/science.2028256 · Cited by 2,061
Self-citationInduction of Ectopic Eyes by Targeted Expression of the eyeless Gene in Drosophila
Halder, G., Callaerts, P., & Gehring, W. J. (1995) · Science · doi:10.1126/science.7892602 · Cited by 1,573
Pax-6, a murine paired box gene, is expressed in the developing CNS
Walther, C., & Gruss, P. (1991) · Development · doi:10.1242/dev.113.4.1435 · Cited by 1,255
Sequence-specific recognition of double helical nucleic acids by proteins.
Seeman, N. C., Rosenberg, J. M., & Rich, A. (1976) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.73.3.804 · Cited by 1,125
Homology of the eyeless Gene of Drosophila to the Small eye Gene in Mice and Aniridia in Humans
Quiring, R., Walldorf, U., Kloter, U., & Gehring, W. J. (1994) · Science · doi:10.1126/science.7914031 · Cited by 1,100
Crystal structure of a yeast TBP/TATA-box complex
Kim, Y., Geiger, J. H., Hahn, S., & Sigler, P. B. (1993) · Nature · doi:10.1038/365512a0 · Cited by 1,084
Cited by
Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
Soufi, A., Garcia, M. F., Jaroszewicz, A., Osman, N., Pellegrini, M., & Zaret, K. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.017 · Cited by 780
“The bipartite domain-Pax family of TFs can bind DNA using both domains and still occupy half of the DNA surface and would therefore be compatible with nucleosome binding (Garvie et al., 2001; Xu et al., 1999) (Figure S7, right, compared to POU TFs).”
Xu, H. E., Lambert, M. H., Montana, V. G., Plunket, K. D., Moore, L. B., Collins, J. L., Oplinger, J. A., Kliewer, S. A., Gampe, R. T., McKee, D. D., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.241410198 · Cited by 538
Self-citationGlobal reference mapping of human transcription factor footprints
Vierstra, J., Lazar, J., Sandstrom, R., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Haugen, E., et al. (2020) · Nature · doi:10.1038/s41586-020-2528-x · Cited by 386
Recognition of Specific DNA Sequences
Garvie, C. W., & Wolberger, C. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00392-6 · Cited by 357
Bhatia, S., Bengani, H., Fish, M., Brown, A., Divizia, M. T., de Marco, R., Damante, G., Grainger, R., van Heyningen, V., & Kleinjan, D. A. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.028 · Cited by 196
Metadata
- Authors
- Xu, H. E., Rould, M. A., Xu, W., Epstein, J. A., Maas, R. L., & Pabo, C. O.
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1999-05-15
- Volume
- 13
- Issue
- 10
- Pages
- 1263-1275
- ISSN
- 0890-9369 (ISSN-L)
- OpenAlex
- W2070250500
- Cited by
- 310
- References
- 71
- Type
- posted content
- Language
- en
- Open access
- diamond
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- Xu, H. E., Rould, M. A., Xu, W., Epstein, J. A., Maas, R. L., & Pabo, C. O. (1999). Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. Genes & Development. https://doi.org/10.1101/gad.13.10.1263
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