The DCX-domain tandems of doublecortin and doublecortin-like kinase

Nature Structural Biology

Volumn 10, Issue 5, 2003, Pages 324-333

  Kim, Myung Hee ^a   Cierpicki, Tomasz ^b   Derewenda, Urszula ^a   Krowarsch, Daniel ^b   Feng, Yuanyi ^c   Devedjiev, Yancho ^a   Dauter, Zbigniew ^d   Walsh, Christopher A ^c   Otlewski, Jacek ^a,b   Bushweller, John H ^a   Derewenda, Zygmunt S ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF WROC AW   (Poland)

^c BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^d BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLECORTIN; DOUBLECORTIN LIKE KINASE; GUANOSINE TRIPHOSPHATASE; PHOSPHOTRANSFERASE; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; GENE MUTATION; HUMAN; HYDRODYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN STABILITY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; BRAIN; CA(2+)-CALMODULIN DEPENDENT PROTEIN KINASE; CONSERVED SEQUENCE; HUMANS; MALE; MICROTUBULE-ASSOCIATED PROTEINS; MICROTUBULES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NERVE TISSUE PROTEINS; NEUROPEPTIDES; PHOSPHOPROTEINS; PROTEIN CONFORMATION; PROTEIN-SERINE-THREONINE KINASES; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

ANIMALIA;

EID: 0242501574     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb918     Document Type: Article

References (55)

1. Nogales, E. Structural insight into microtubule function. Annu. Rev. Biophys. Biomol. Struct. 30, 397-420 (2001).
2. Mandelkow, E. & Mandelkow, E.M. Microtubules and microtubule-associated proteins. Curr. Opin. Cell Biol. 7, 72-81 (1995).
3. Gleeson, J.G. et al. doublecortin, a brain-specific gene mutated in human Xlinked lissencephaly and double cortex syndrome, encodes a putative signaling protein. Cell 92, 63-72 (1998).
4. des Portes, V. et al. A novel CNS gene required for neuronal migration and involved in X-linked subcortical laminar heterotopia and lissencephaly syndrome. Cell 92, 51-61 (1998).
5. Raymond, A.A. et al. Abnormalities of gyration, heterotopias, tuberous sclerosis, focal cortical dysplasia, microdysgenesis, dysembryoplastic neuroepithelial tumour and dysgenesis of the archicortex in epilepsy. Clinical, EEG and neuroimaging features in 100 adult patients. Brain 118, 629-660 (1995).
6. Francis, F. et al. doublecortin is a developmentally regulated, microtubuleassociated protein expressed in migrating and differentiating neurons. Neuron 23, 247-256 (1999).
7. Gleeson, J.G., Lin, RT., Flanagan, L.A. & Walsh, C.A. doublecortin is a microtubule-associated protein and is expressed widely by migrating neurons. Neuron 23, 257-271 (1999).
8. Dobyns, W.B. & Truwit, C.L. Lissencephaly and other malformations of cortical development: 1995 update. Neuropediatrics 26, 132-147 (1995).
9. Dobyns, W.B., Reiner, O., Carrozzo, R. & Ledbetter, D.H. Lissencephaly. A human brain malformation associated with deletion of the LI51 gene located at chromosome 17p13. J. Am. Med. 270, 2838-2842 (1993).
10. Sapir, T. et al. doublecortin mutations cluster in evolutionarily conserved functional domains. Hum. Mol. Genet. 9, 703-712 (2000).
11. Taylor, K.R., Holzer, A.K., Bazan, J.R., Walsh, C.A. & Gleeson, J.G. Patient mutations in doublecortin define a repeated tubulin-binding domain. J. Biol. Chem. 275, 34442-34450 (2000).
12. Burgess, H.A. & Reiner, O. doublecortin-like kinase is associated with microtubules in neuronal growth cones. Mol. Cell. Neurosci. 16, 529-541 (2000).
13. Burgess, H.A., Martinez, S. & Reiner, O. KIAA0369, doublecortin-like kinase, is expressed during brain development. J. Neurosci. Res. 58, 567-575 (1999).
14. Lin, P.T., Gleason, J.G., Corbo, J.C., Flanagan, L. & Walsh, C.A. DCAMKL1 encodes a protein kinase with homology to doublecortin that regulates microtubule polymerization. J. Neurosci. 20, 9152-9161 (2000).
15. Schultz, J., Copley, R.R., Doerks, T., Ponting, C.P. & Bork, P. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28, 231-234 (2000).
16. Gonczy, P. et al. zyg-8, a gene required for spindle positioning in C. elegans, encodes a doublecortin-related kinase that promotes microtubule assembly. Dev. Cell 1, 363-375 (2001).
17. Sullivan, L.S. et al. Mutations in a novel retina-specific gene cause autosomal dominant retinitis pigmentosa. Nat. Genet. 22, 255-259 (1999).
18. 15N resonances of the N-terminal microtubule-binding domain of human doublecortin. J. Biomol. NMR 25, 81-82 (2003).
19. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138 (1993).
20. Huang, L., Hofer, F., Martin, G.S. & Kim, S.H. Structural basis for the interaction of Ras with RalGDS. Nat. Struct. Biol. 5, 422-426 (1998).
21. Ito, T., Matsui, Y., Ago, T., Ota, K. & Sumimoto, H. Novel modular domain PB1 recognizes PC motif to mediate functional protein-protein interactions. EMBO J. 20, 3938-3946 (2001).
22. Terasawa, H. et al. Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif. EMBO J. 20, 3947-3956 (2001).
23. Buchberger, A., Howard, M.J., Proctor, M. & Bycroft, M. The UBX domain: a widespread ubiquitin-like module. J. Mol. Biol. 307, 17-24 (2001).
24. Vijay-Kumar, S., Bugg, C.E., & Cook, W. J. Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol. 194, 531-544 (1987).
25. Scheffzek, K. et al. The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast. Structure 9, 1043-1050 (2001).
26. Uversky, V.N. Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11, 739-756 (2002).
27. Semisotnov, G.V. et al. Study of the "molten globule" intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers 31, 119-128 (1991).
28. Itzhaki, L.S., Evans, P.A., Dobson, C.M. & Radford, S.E. Tertiary interactions in the folding pathway of hen lysozyme: kinetic studies using fluorescent probes. Biochemistry 33, 5212-5220 (1994).
29. Engelhard, M. & Evans, P.A. Kinetics of interaction of partially folded proteins with a hydrophobic dye: evidence that molten globule character is maximal in early folding intermediates. Protein Sci. 4, 1553-1562 (1995).
30. Eliezer, D. & Wright, P.E. Is apomyoglobin a molten globule? Structural characterization by NMR. J. Mol. Biol. 263, 531-538 (1996).
31. Kitahara, R., Yamada, H., Akasaka, K. & Wright, P.E. High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded. J. Mol. Biol. 320, 311-319 (2002).
32. Horesh, D. et al. doublecortin, a stabilizer of microtubules. Hum. Mol. Genet. 8, 1599-1610 (1999).
33. Yoshiura, K., Noda, Y., Kinoshita, A. & Niikawa, N. Colocalization of doublecortin with the microtubules: an ex vivo colocalization study of mutant doublecortin. J. Neurobiol. 43, 132-139 (2000).
34. Fygenson, D.K., Flyvbjerg, H., Sneppen, K, & Libchaber, A. Spontaneous nucleation of microtubules. Phys. Rev. E 51, 5058-5063 (1995).
35. Fygenson, D.K., Braun, E. & Libchaber, A. Phase diagram of microtubules. Phys. Rev. E 50, 1579-1588 (1994).
36. Krawczak, M. & Cooper, D.N. The human gene mutation database. Trends Genet. 13, 121-122 (1997).
37. Sheffield, P., Garrard, S. & Derewenda, Z. Overcoming expression and purification problems of RhoGDI using a family of 'parallel' expression vectors. Protein Expr. Purif. 15, 34-39 (1999).
38. Wang, W. & Malcolm, B.A. Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange site-directed mutagenesis. Biotechniques 26, 680-682 (1999).
39. Delaglio, F., Kontaxis, G. & Bax, A. Protein structure determination using molecular replacement and NMR dipolar couplings. J. Am. Chem. Soc. 122, 2142-2143 (2000).
40. Goddard, T.D. & Kneller, D.G. SPARKY 3 (University of California, San Francisco; 2002).
41. Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298 (1997).
42. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54, 905-921 (1998).
43. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289-302 (1999).
44. Nilges, M., Macias, M.J., O'Donoghue, S.I. & Oschkinat, H. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J. Mol. Biol. 269, 408-422 (1997).
45. Kim, M.H., Derewenda, U., Devedjiev, Y., Dauter, Z. & Derewenda, Z.S. Purification and crystallization of the N-terminal domain from the human doublecortin-like kinase. Acta Crystallogr. D 59, 502-505 (2003).
46. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
47. Sheldrick, G.M. & Gould, R.O. Structure solution by iterative peaklist optimisation and tangent expansion in space group P1. Acta Crystallogr. B 51, 423-431 (1995).
48. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
49. Fortelle, E.D.L. & Bricogne, G. Maximum-likelihood heavy atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494 (1997).
50. Abrahams, J.P. & Leslie, A.G.W. Methods used in the structure determination of bovine mitochondrial F1 ATPase, Acta Crystallogr. D 52, 30-42 (1996).
51. Perrakis, A., Morris, R. & Lamzin, V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458-463 (1999).
52. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255 (1997).
53. Navaza, J. AMoRE: an automated package for molecular replacement. Acta Crystallogr. A 50, 157-163 (1994).
54. Laskowski, R.A., McArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J, Appl. Crystallogr. 26, 282-291 (1993).
55. Santoro, M.M. & Bolen, D.W. A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range. Biochemistry 31, 4901-4907 (1992).