High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations

EMBO Journal

Volumn 25, Issue 18, 2006, Pages 4187-4194

  Kikkawa, Masahide ^a   Hirokawa, Nobutaka ^b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Cryo electron microscopy; Kinesin; Microtubule

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ADENYLYLIMIDODIPHOSPHATE; KINESIN; MOLECULAR MOTOR; NUCLEOTIDE BINDING PROTEIN;

ARTICLE; BINDING KINETICS; CELL TRANSPORT; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; ELECTRON MICROSCOPE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; IMAGE ANALYSIS; MICROTUBULE; NUCLEOTIDE BINDING POCKET; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; HUMANS; KINESIN; MACROMOLECULAR SUBSTANCES; MICROTUBULES; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR MOTOR PROTEINS; NERVE TISSUE PROTEINS; NUCLEOTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; TUBULIN;

EID: 33748931452     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/sj.emboj.7601299     Document Type: Article

References (40)

1. Al-Bassam J, Cui Y, Klopfenstein D, Carragher BO, Vale RD, Milligan RA (2003) Distinct conformations of the kinesin Unc104 neck regulate a monomer to dimer motor transition. J Cell Biol 163: 743-753
2. Carter NJ, Cross RA (2005) Mechanics of the kinesin step. Nature 435: 308-312
3. Chacon P, Wriggers W (2002) Multi-resolution contour-based fitting of macromolecular structures. J Mol Biol 317: 375-384
4. Garcia-Saez I, Yen T, Wade RH, Kozielski F (2004) Crystal structure of the motor domain of the human kinetochore protein CENP-E. J Mol Biol 340: 1107-1116
5. Hackney DD (1988) Kinesin ATPase: rate-limiting ADP release. Proc Natl Acad Sci USA 85: 6314-6318
6. Hackney DD (2005) The tethered motor domain of a kinesin-microtubule complex catalyzes reversible synthesis of bound ATP. Proc Natl Acad Sci USA 102: 18338-18343
7. Hackney DD, Stock MF, Moore J, Patterson RA (2003) Modulation of kinesin half-site ADP release and kinetic processivity by a spacer between the head groups. Biochemistry 42: 12011-12018
8. Higuchi H, Bronner CE, Park HW, Endow SA (2004) Rapid double 8-nm steps by a kinesin mutant. EMBO J 23: 2993-2999
9. Hirokawa N (1998) Kinesin and dynein superfamily proteins and the mechanism of organelle transport. Science 279: 519-526
10. Kamei T, Kakuta S, Higuchi H (2005) Biased binding of single molecules and continuous movement of multiple molecules of truncated single-headed kinesin. Biophys J 88: 2068-2077
11. Kikkawa M, Okada Y, Hirokawa N (2000) 15 Å resolution model of the monomeric kinesin motor, KIF1A. Cell 100: 241-252
12. Kikkawa M, Sablin EP, Okada Y, Yajima H, Fletterick RJ, Hirokawa N (2001) Switch-based mechanism of kinesin motors. Nature 411: 439-445
13. Kleywegt G, Jones T (1994) A super position. CCP4/ESF-EACBM Newsletter on Protein Crystallography. Vol. 31, pp 9-14
14. Klumpp LM, Hoenger A, Gilbert SP (2004) Kinesin's second step. Proc Natl Acad Sci USA 101: 3444-3449
15. Krebs A, Goldie KN, Hoenger A (2004) Complex formation with kinesin motor domains affects the structure of microtubules. J Mol Biol 335: 139-153
16. Lawson JD, Pate E, Rayment I, Yount RG (2004) Molecular dynamics analysis of structural factors influencing back door pi release in myosin. Biophys J 86: 3794-3803
17. Li H, DeRosier DJ, Nicholson WV, Nogales E, Downing KH (2002) Microtubule structure at 8 Å resolution. Structure 10: 1317-1328
18. Lowe J, Li H, Downing KH, Nogales E (2001) Refined structure of alpha beta-tubulin at 3.5 Å resolution. J Mol Biol 313: 1045-1057
19. Ma YZ, Taylor EW (1997) Kinetic mechanism of a monomeric kinesin construct. J Biol Chem 272: 717-723
20. Metlagel Z, Kikkawa YS, Kikkawa M (2006) Ruby-helix: an implementation of helical image processing based on object-oriented scripting language. J Struc Biol (in press)
21. Mindell JA, Grigorieff N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142: 334-347
22. Naber N, Minehardt TJ, Rice S, Chen X, Grammer J, Matuska M, Vale RD, Kollman PA, Car R, Yount RG, Cooke R, Pate E (2003) Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules. Science 300: 798-801
23. Nitta R, Kikkawa M, Okada Y, Hirokawa N (2004) KIF1A alternately uses two loops to bind microtubules. Science 305: 678-683
24. Nogales E, Wolf SG, Downing KH (1998) Structure of the alpha beta tubulin dimer by electron crystallography. Nature 391: 199-203
25. Ogawa T, Nitta R, Okada Y, Hirokawa N (2004) A common mechanism for microtubule destabilizers-M type kinesins stabilize curling of the protofilament using the class-specific neck and loops. Cell 116: 591-602
26. Okada Y, Higuchi H, Hirokawa N (2003) Processivity of the single-headed kinesin KIF1A through biased binding to tubulin. Nature 424: 574-577
27. Okada Y, Hirokawa N (1999) A processive single-headed motor: kinesin superfamily protein KIF1A. Science 283: 1152-1157
28. Rice S, Lin AW, Safer D, Hart CL, Naber N, Carragher BO, Cain SM, Pechatnikova E, Wilson-Kubalek EM, Whittaker M, Pate E, Cooke R, Taylor EW, Milligan RA, Vale RD (1999) A structural change in the kinesin motor protein that drives motility. Nature 402: 778-784
29. Sack S, Muller J, Marx A, Thormahlen M, Mandelkow EM, Brady ST, Mandelkow E (1997) X-ray structure of motor and neck domains from rat brain kinesin. Biochemistry 36: 16155-16165
30. Sindelar CV, Budny MJ, Rice S, Naber N, Fletterick R, Cooke R (2002) Two conformations in the human kinesin power stroke defined by X-ray crystallography and EPR spectroscopy. Nat Struct Biol 9: 844-848
31. Skiniotis G, Cochran JC, Muller J, Mandelkow E, Gilbert SP, Hoenger A (2004) Modulation of kinesin binding by the C-termini of tubulin. EMBO J 23: 989-999
32. Taniguchi Y, Nishiyama M, Ishii Y, Yanagida T (2005) Entropy rectifies the Brownian steps of kinesin. Nat Chem Biol 1: 342-347
33. Uemura S, Ishiwata S (2003) Loading direction regulates the affinity of ADP for kinesin. Nat Struct Biol 10: 308-311
34. Vale RD, Milligan RA (2000) The way things move: looking under the hood of molecular motor proteins. Science 288: 88-95
35. van Heel M (1986) Similarity measures between images. Ultramicroscopy 21: 95-100
36. Vinogradova MV, Reddy VS, Reddy AS, Sablin EP, Fletterick RJ (2004) Crystal structure of kinesin regulated by Ca(2+)-calmodulin. J Biol Chem 279: 23504-23509
37. Woehlke G, Ruby AK, Hart CL, Ly B, Hom-Booher N, Vale RD (1997) Microtubule interaction site of the kinesin motor. Cell 90: 207-216
38. Yan Y, Sardana V, Xu B, Homnick C, Halczenko W, Buser CA, Schaber M, Hartman GD, Huber HE, Kuo LC (2004) Inhibition of a mitotic motor protein: where, how, and conformational consequences. J Mol Biol 335: 547-554
39. Yonekura K, Toyoshima C (2000) Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes. Ultramicroscopy 84: 15-28
40. Yun M, Zhang X, Park CG, Park HW, Endow SA (2001) A structural pathway for activation of the kinesin motor ATPase. EMBO J 20: 2611-2618