Structures of EF-hand Ca2+-binding proteins: Diversity in the organization, packing and response to Ca2+ binding

BioMetals

Volumn 11, Issue 4, 1998, Pages 297-318

  Nelson, Melanie R ^a   Chazin, Walter J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Ca2+ signaling; Ca2+ binding protein; Calmodulin; EF hand; Protein structure; Signal transduction

Indexed keywords

CALCIUM BINDING PROTEIN;

ARTICLE; DATA BASE; HUMAN; NONHUMAN; PROTEIN TERTIARY STRUCTURE; PROTEIN VARIANT; SENSOR; SIGNAL TRANSDUCTION;

ANIMALS; BINDING SITES; CALCIUM; CALCIUM-BINDING PROTEINS; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

EID: 0032462546     PISSN: 09660844     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1009253808876     Document Type: Article

References (98)

1. Ahmed FR, Rose DR, Evans SV, Pippy ME, To R. 1993 Refinement of recombinant oncomodulin at 1.30 Å resolution. J Mol Biol 230, 1216-1224
2. 1.11.2 binding pathway. J Mol Biol 252, 102-121
3. Ames JB, Ishima R, Tanaka T, Gordon JI, Stryer L, Ikura M. 1997 Molecular mechanics of calcium-myristoyl switches. Nature 389, 198-202
4. Ames JB, Porumb T, Tanaka T, Ikura M, Stryer L. 1995 Amino-terminal myristoylation induces cooperative calcium binding to recoverin. J Biol Chem 270, 4526-4533
5. Ames JB, Tanaka T, Stryer L, Ikura M. 1996 Portrait of a myristoyl-switch protein. Curr Opin Struct Biol 6, 432-438
6. 9k. Protein Sci 6, 1139-1147
7. Babu YS, Bugg CE, Cook WJ. 1988 Structure of calmodulin refined at 2.2 Å resolution. J Mol Biol 204, 191-204
8. Bagshaw CR, Kendrick-Jones J. 1979 Characterization of homologous divalent metal ion binding sites of vertebrate and molluscan myosins using electro paramagnetic resonance spectroscopy. J Mol Biol 130, 317-336
9. 1H 2-D NMR. A comparison of the calcium and magnesium loaded forms. Biochimie 74, 837-844
10. 15N relaxation using inverse deteced two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry 31, 5269-5278
11. Bayley PM, Findlay WA, Martin SR. 1996 Target recognition by calmodulin: Dissecting the kinetics and affinity of interaction using short peptide sequences. Protein Sci 5, 1215-1228
12. 2+-induced conformational changes. Nature Struct Biol 4, 532-538
13. 2+-binding domain VI of rat calpain is a homodimer in solution: hydrodynamic, crystallization and preliminary X-ray diffraction studies. ProteinSci 5, 533-537
14. 1H 2D NMR. Biochemistry 32, 1302-1309
15. Chattopadhyaya R, Meador W, Means A, Quiocho F. 1992 Calmodulin structure refined at 1.7 Å resolution. J Mol Biol 228, 1177-1192
16. 2+-dependent interaction of recoverin and rhodopsin kinase. J Biol Chem 18060-18066
17. Cheney RE, Mooseker MS. 1992 Unconventional myosins. Curr Opin Cell Biol 4, 27-35
18. Clipstone NA, Crabtree GR. 1992 Identification of calcineurin as a key signalling enzyme in T-lymphocyte activation. Nature 357, 695-697
19. Cook WJ, Jeffrey LC, Cox JA, Vijay-Kumar S. 1993 Structure of a sarcoplasmic calcium-binding protein from amphioxus refined at 2.4 Å resolution. J Mol Biol 229, 461-471
20. Cox JA, Stein EA. 1981 Characterization of a new sarcoplasmic calcium-binding protein with magnesium-induced cooperativity in the binding of calcium. Biochemistry 20, 5430-5436
21. Crawford C, Brown NR, Willis AC. 1993 Studies of the active site of m-calpain and the interaction with calpastatin. Biochem J 296, 135-142
22. Crivici A, Ikura M. 1995 Molecular and structural basis of target recognition by calmodulin. Annu Rev Biophys Biomol Struct 24, 85-116
23. Declercq J-P, Tinant B, Parello J, Rambaud J. 1991 Ionic interactions with parvalbumins: crystal structure determination of pike 4.10 parvalbumin in four different ionic environments. J Mol Biol 220, 1017-1039
24. Drohat AC, Amburgey JC, Abildgaard F, Starich MR, Baldisseri D, Weber DJ. 1996 Solution structure of rat apo-S100B(ββ) as determined by NMR spectroscopy. Biochemistry 35, 11577-11588
25. Drohat AC, Baldisseri DM, Rustandi RR, Weber DJ. 1998 Solution structure of calcium-bound rat S100B(ββ) as determined by nuclear magnetic resonance spectroscopy. Biochemistry 37, 2729-2740
26. Engelborghs Y, Mertens K, Willaert K, Luan-Rilliet Y, Cox JA. 1990 Kinetics of conformational changes in Nereis sarcoplasmic calcium-binding protein upon binding of divalent ions. J Biol Chem 265, 18809-18815
27. 2+-saturated state. Biochemistry 36, 3448-3457
28. Findlay WA, Martin SM, Beckingham K, Bayley PM. 1995 Recovery of native structure by calcium binding site mutants of calmodulin upon binding of sk-MLCK target peptides. Biochemistry 34, 2087-2094
29. Finn BE, Evënas J, Crakenberg T, Waltho JP, Thulin E, Forsén S. 1995 Calcium-induced structural changes and domain autonomy in calmodulin. Nature Struct Biol 2, 777-783
30. Flaherty KM, Zozulya S, Stryer L, McKay DB. 1993 Three-dimensional structure of recoverin, a calcium sensor in vision. Cell 75, 709-716
31. Gagné S, Tsuda S, Li M, Smillie L, Sykes B. 1995 Structures of the troponin C regulatory domains in the apo and calcium-saturated states. Nature Struct Biol 2, 784-789
32. Gagné SM, Li MX, Sykes BD. 1997 Mechanism of direct coupling between binding and induced structural change in regulatory calcium binding proteins. Biochemistry 36, 4386-4392
33. Griffith JP, Kim JL, Kim EE, Sintchak MD, Thomson JA, Fitzgibbon MJ, Fleming MA, Caron PR, Hsiao K, Navia MA. 1995 X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKB12-FK506 complex. Cell 82, 507-522
34. Haiech J, Kilhoffer M-C, Lukas TJ, Craig TA, Roberts DM, Watterson DM. 1991 Restoration of calcium binding activity of mutant calmodulins toward normal by presence of a calmodulin binding structure. J Biol Chem 266, 3427-3431
35. Heidorn DB, Trewhella J. 1988 Comparison of the crystal and solution structures of calmodulin and troponin C. Biochemistry 27, 909-915
36. Hermann A, Cox JA. 1995 Sarcoplasmic calcium-binding protein. Comp Biochem Biophys Res Comm 235, 271-275
37. Herzberg O, James MNG. 1985 Structure of the calcium regulatory muscle protein troponin-C at 2.8 Å resolution. Nature 313, 653-659
38. Herzberg O, James MNG. 1988 Refined crystal structure of troponin C from turkey skeletal muscle at 2.0 Å resolution. J Mol Biol 203, 761-779
39. 2+-induced conformational transition of troponin C. J Biol Chem 261, 2638-2644
40. 2+-binding module in BM-40. Nature Struct Biol 3, 67-73
41. Hohenester E, Maurer P, Timpl R. 1997 Crystal structure of a pair of follistatin-like and EF-hand calcium-binding domains in BM-40. EMBO J 16, 3778-3786
42. Houdusse A, Cohen C. 1996 Structure of the regulatory domain of scallop myosin at 2 Å resolution: implications for regulation. Structure 4, 21-32
43. 2+-switch in the calmodulin superfamily. Structure 5, 1695-1711
44. 2+-free calmodulin binding to unconventional myosins reveals how calmodulin acts as a regulatory switch. Structure 4, 1475-1490
45. Ikura M, Clore GM, Gronenborn AM, Zhu G, Klee CB, Bax A. 1992 Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science 256, 632-638
46. Jansco A, Szent-Gyorgyi AG. 1994 Regulation of scallop myosin by the regulatory light chain depends on a single glycine residue. Proc Natl Acad Sci USA 91, 8762-8766
47. 9k's, as determined by NMR, show that the calcium-binding site can adopt different folds. Biochemistry 32, 8429-8438
48. Kennedy MT, Brockman H, Rusnak F. 1996 Contributions of myristoylation to calcineurin structure/function. J Biol Chem 271, 26517-26521
49. Kilby PM, Van Eldik LJ, Roberts GCK. 1996 The solution structure of the bovine S100B protein dimer in the calcium-free state. Structure 4, 1041-1052
50. Kissinger CR, Parge HE, Knighton DR, Lewis CT, Pelletier LA, Tempczyk A, Kalish VJ, Tucker KD, Showalter RE, Moomaw EW, Gastinel LN, Hakuba N, Chen X, Maldonado F, Barker JE, Bacquet R, Villafranca JE. 1995 Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex. Nature 378, 641-644
51. Klee CB, Draetta GF, Hubbard MJ. 1988 Calcineurin. Adv Enzymol 61, 149-200
52. Klee CB, Krinks MH. 1978 Purification of cyclic 3′,5′-nucleotide phosphodiesterase inhibitory protein by affinity chromotography on activator protein coupled to sepharose. Biochemistry 17, 120-126
53. Klenchin VA, Calvert PD, Bownds MD. 1995 Inhibition of rhodopsin kinase by recoverin. J Biol Chem 270, 16147-16152
54. 9k. J Mol Biol 231, 711-734
55. Kretsinger RH, Nockolds CE. 1973 Carp muscle calcium-binding protein: II. structure determination and general description. J Biol Chem 248, 3313-3326
56. Kuboniwa H, Tjandra N, Grzesiek S, Ren H, Klee CB, Bax A. 1995 Solution structure of calcium-free calmodulin. Nature Struct Biol 2, 768-776
57. Lin G-d, Chattopdhyaya D, Masatoshi M, Wang KKW, Carson M, Jin L, Yuen P-w, Takano E, Hatanaka M, DeLucas LJ, Narayana SVL. 1997 Crystal structure of calcium bound domain VI of calpain at 1.9 Å resolution and its role in enzyme assembly, regulation, and inhibitor binding. Nature Struct Biol 4, 539-547
58. 9k. Biochemistry 26, 6723-6735
59. 28k as determined from the association of six synthetic EF-hand fragments. Protein Sci 6, 2385-2396
60. Liu J, Farmer JD, Jr. Lane, W.S. Firedman, J. Weissman, I. Schreiber SL. 1991 Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes. Cell 66, 807-815
61. Martin SR, Bayley PM, Brown SE, Porumb T, Zhang M, Ikura M. 1996 Spectoscopic characterization of a high-affinity calmodulin-target peptide hybrid molecule. Biochemistry 35, 3508-3517
62. Matsumura H, Shiba T, Inoue T, Harada S, Kai Y. 1998 A novel mode of target recognition suggested by the 2.0 Å structure of holo S100B from bovine brain. Structure 6, 233-241
63. McPhalen CA, Sielecki AR, Santarsiero James. 1994 Refined crystal structure of rat parvalbumin, a mammalian alpha-lineage parvalbumin, at 2.0 Å resolution. J Mol Biol 235, 718-732
64. McPhalen CA, Strynadka NCJ, James MNG. 1991 Calcium-binding sites in proteins: a structural perspective. Adv Prot Chem 42, 77-144
65. Meador WE, Means AR, Quiocho FA. 1992 Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin-peptide complex. Science 257, 1251-1255
66. Meador WE, Means AR, Quiocho FA. 1993 Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structures. Science 262, 1718-1721
67. 2+ sensor proteins. Protein Sci 7, 270-282
68. Nishimura T, Goll DE. 1991 Binding of calpain fragments to calpastatin. J Biol Chem 266, 11842-11850
69. O'Keefe SJ, Tamura J, Kincaid RL, Tocci MJ, O'Neill EA. 1992 FK-506- and CsA-sensitive activation of the interleukin-2 promoter by calcineurin. Nature 692-694
70. O'Neil KT, DeGrado WF. 1990 How calmodulin binds its targets: sequence independent recognition of amphiphilic alpha-helices. Trends Biochem Sci 15, 59-64
71. Parmyakov EA, Medvedkin VN, Mitin YV, Kretsinger RH. 1991 Noncovalent complex between domain AB and domains CD*EF of parvalbumin. Biochim Biophys Acta 1076, 67-70
72. 2+-binding proteins parvalbumin and oncomodulin and their genes: new structural and functional findings. Biochim Biophys Acta 1306, 39-54
73. 2+-binding proteins. Nature Struct Biol 2, 790-796
74. 2+ ion. FEBS Letters 395, 89-94
75. Rayment I, Rypniewski WR, Schmidt-Base K, Smith R, Tomchick DR, Benning MM, Winkelmann DA, Wesenberg G, Holden HM. 1993 Three-dimensional structure of myosin subfragment-I: a molecular motor. Science 261, 50-58
76. 2+-dependent interaction of S100B(ββ) with a peptide derived from p53. Biochemistry 37, 1951-1960
77. Satyshur K, Rao S, Pyzalska D, Drendel W, Greaser M, Sundraralingam M. 1988 Refined structure of chicken skeletal muscle troponin C in the two-calcium state at 2 Å resolution. J Biol Chem 263, 1628-1647
78. 2+-signal transduction by S100 proteins. Structure 6, 223-231
79. Sellers JA, Goodson HV. 1995 Motor proteins 2: myosin. Protein Profile 2, 1323-1423
80. 1H NMR structural evidence. Science 249, 280-283
81. Sia SK, Li MX, Spyracopoulos L, Gagné SM, Liu W, Putkey JA, Sykes BD. 1997 Structure of cardiac muscle troponin C unexpectedly reveals a closed regulatory domain. J Biol Chem 272, 18216-182121
82. 2+-binding Proteins. Nature Struct Biol 1, 239-245.
83. 9k by NMR spectroscopy. J Mol Biol 249, 441-462
84. Smith SP, Shaw GS. 1998 A novel calcium-sensitive switch revealed by the structure of human S100B in the calcium-bound form. Structure 6, 211-222
85. Spera S. I., Mitsuhiko I, Bax A. 1991 Measurement of the exchange rates of rapidly exchanging amide protons: Application to the study of calmodulin and its complex with a myosin light chain kinase fragment. J Biomol NMR 1, 155-165
86. Spyracopoulos L, Li, M.X. Sia, S.K. Gangne, S.M. Chandra, M. Solaro, R.J. Sykes. 1997 Calcium-induced structural transition in the regulatory domain of human cardiac troponin C. Biochemistry 36, 12138-12146
87. Strynadka NCJ, James MNG. 1989 Crystal structures of the helix-loop-helix calcium-binding proteins. Annu Rev Biochem 58, 951-998
88. Strynadka NCJ, Cherney M, Sielecki AR, Li MX, Smillie LB, James MNG. 1997 Structural details of a calcium-induced molecular switch: X-ray crystallographic analysis of the calcium-saturated N-terminal domain of troponin C at 1.75 Å resolution. J Mol Biol 273, 238-255
89. Swindells MB, Ikura M. 1996 Pre-formation of the semi-open conformation by the apo-calmodulin C-terminal domain and implications for binding IQ motifs. Nature Struct Biol 3, 501-504
90. Szebenyi DME, Moffat K. 1986 The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. J Biol Chem 261, 8761-8777
91. Szent-Györgyi AG, Chantler PD. 1994 Control of contraction by calcium binding to myosin. In: Engel AG, Franzini-Armstrong C, eds. Myology, vol. 2. McGraw-Hill: 506-528
92. Tanaka T, Ames JB, Harvey TS, Stryer L, Ikura M. 1995 Sequestration of the membrane-targeting myristoyl group of recoverin in the calcium-free state. Nature 376, 444-446
93. Tjandra N, Kubinowa H, Bax A. 1995 Rotational dynamics of calcium-free calmodulin by 15N-NMR relaxation measurements. Eur J Biochem 230, 1014-1024
94. Upson C, Faulheber T Jr, Kamins D, Laidlaw D, Schlegel D, Vroom J, Gurwitz R, van Dam A. 1989 The application visualization system: A computational environment for scientific visualization. Comput Graphics Appl 9, 30-42
95. Vijay-Kumar S, Cook WJ. 1992 Structure of a sarcoplasmic calcium-binding protein from Nereis divisicolor refined at 2.0 Å resolution. J Mol Biol 224, 413-426
96. 9k: NMR studies of the N56A mutant. Protein Sci 4, 1045-1055
97. Xie X, Harrison DH, Schlichting I, Sweet RM, Kalabokis VN, Szent-Gyorgyi AG. 1994 Structure of the regulatory domain of scallop myosin at 2.8 angstrom resolution. Nature 368, 306-312
98. Zhang M, Tanaka T, Ikura M. 1995 Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nature Struct Biol 2, 758-767