Metal-free and Ca2+-bound structures of a multidomain EF-hand protein, CBP40, from the lower eukaryote Physarum polycephalum

Structure

Volumn 11, Issue 1, 2003, Pages 75-85

  Iwasaki, Wakana ^a   Sasaki, Hiroshi ^b   Nakamura, Akio ^c   Kohama, Kazuhiro ^c   Tanokura, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c GUNMA UNIVERSITY   (Japan)

Author keywords

Calcium binding protein 40; Calcium binding proteins; Crystal structure; EF hand; Physarum polycephalum

Indexed keywords

CALCIUM BINDING PROTEIN; CALCIUM BINDING PROTEIN 40; CALCIUM ION; EF HAND PROTEIN; METAL; PROTEIN; UNCLASSIFIED DRUG; CALCIUM; CALMODULIN; CALPAIN; CBP40 PROTEIN, PHYSARUM; PROTOZOAL PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; EUKARYOTE; HYDROPHOBICITY; OLIGOMERIZATION; PHYSARUM POLYCEPHALUM; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; AMINO ACID SEQUENCE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SWINE;

CHONDROMYCES; EUKARYOTA; MYXOGASTRIA; PHOCIDAE; PHYSARUM; PHYSARUM POLYCEPHALUM;

AMINO ACID SEQUENCE; ANIMALS; CALCIUM; CALCIUM-BINDING PROTEINS; CALMODULIN; CALPAIN; METALS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; SEQUENCE ALIGNMENT; SWINE;

EID: 0642284474     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(02)00932-2     Document Type: Article

References (48)

1. Sauer, H.W. (1982). Developmental Biology of Physalum. (Cambridge: Cambridge University Press), pp. 1-237.
2. Jarosch R. Screw-mechanical models related to cytoplasmic streaming. Protoplasma Suppl. 1:1988;15-26.
3. Kamiya N. Physical and chemical basis of cytoplasmic streaming. Annu. Rev. Plant Physiol. 32:1981;205-236.
4. Mottahedeh J., Marsh R. Characterization of 101-kDa transglutaminase from Physarum polycephalum and identification of LAV1-2 as substrate. J. Biol. Chem. 273:1998;29888-29895.
5. 2+-dependent inhibitory factor Eur. J. Cell Biol. 56:1991;113-122.
6. Okagaki T., Ishikawa R., Kohama K. Purification of a novel Ca-binding protein that inhibits myosin light chain kinase activity in lower eukaryote Physarum polycephalum. Biochem. Biophys. Res. Commun. 176:1991;564-570.
7. Pallota D., Laroche A., Terrier A. Molecular cloning of stage specific mRNAs from amoebae and plasmodia of Physarum polycephalum. Biochem. Cell Biol. 64:1986;1294-1302.
8. Laroche A., Lemieux G., Pallotta D. The nucleotide sequence of a developmentally regulated cDNA from Physarum polycephalum. Nucleic Acids Res. 17:1989;10502.
9. Nakamura A., Okagaki T., Takagi T., Nakashima K., Yazawa M., Kohama K. Calcium binding properties of recombinant calcium binding protein 40, a major calcium binding protein of lower eukaryote Physarum polycephalum. Biochemistry. 39:2000;3827-3834.
10. 2+-binding protein CBP40 from lower eukaryote Physarum polycephalum. Mol. Biol. Cell Suppl. 12:2001;481A.
11. +2-regulation of ATP-dependent interaction between actin and myosin of a lower eukaryote, Physarum polycephalum. J. Biochem. 110:1991;508-513.
12. Nakamura A., Kohama K. Calcium regulation of the actin-myosin interaction of Physarum polycephalum. Int. Rev. Cytol. 191:1999;53-98.
13. Walshaw J., Woolfson D.N. Socket. a program for identifying and analysing coiled-coil motifs within protein structures J. Mol. Biol. 307:2001;1427-1450.
14. Ruoslahti E., Pierschbacher M.D. Arg-Gly-Asp. a versatile cell recognition signal Cell. 44:1986;517-518.
15. Bourdon M.A., Krusius T., Campbell S., Schwartz N.B., Ruoslachti E. Identification and synthesis of a recognition signal for attachment of glycosaminoglycans to proteins. Proc. Natl. Acad. Sci. USA. 84:1987;3194-3198.
16. 2+-induced conformational changes. Nat. Struct. Biol. 4:1997;532-538.
17. Lin G.D., Chattopadhyay D., Maki M., Wang K.K., Carson M., Jin L., Yuen P.W., Takano E., Hatanaka M., DeLucas L.J.et al. Crystal structure of calcium bound domain IV of calpain at 1.9 Å resolution and its role in enzyme assembly, regulation, and inhibitor binding. Nat. Struct. Biol. 4:1997;539-547.
18. Hosfield C.M., Elce J.S., Davies P.L., Jia Z. Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation. EMBO J. 18:1999;6880-6889.
19. Strobl S., Fernandez-Catalan C., Braun M., Huber R., Masumoto H., Nakagawa K., Irie A., Sorimachi H., Bourenkow G., Bartunik H.et al. The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. Proc. Natl. Acad. Sci. USA. 97:2000;588-592.
20. Jia J., Han Q., Borregaard N., Lollike K., Cygler M. Crystal structure of human grancalcin, a member of the penta-EF-hand protein family. J. Mol. Biol. 300:2000;1271-1281.
21. 2+-induced changes in penta-EF-hand proteins Structure. 9:2001;267-275.
22. Babu Y.S., Bugg C.E., Cook W.J. Structure of calmodulin refined at 2.2 Å resolution. J. Mol. Biol. 204:1988;191-204.
23. Nakayama S., Kretsinger R.H. Evolution of the EF-hand family of proteins. Annu. Rev. Biophys. Biomol. Struct. 23:1994;473-507.
24. Iwasaki W., Sasaki H., Nakamura A., Kohama K., Tanokura M. Crystallization and preliminary X-ray diffraction studies of a 40 kDa calcium binding protein specifically expressed in plasmodia of Physarum polycephalum. J. Biochem. 126:1999;7-9.
25. Hohenester E., Maurer P., Timpl R. Crystal structure of a pair of follistatin-like and EF-hand calcium-binding domains of BM-40. EMBO J. 16:1997;3778-3786.
26. 2+, calmodulin, skeletal muscle myosin light chain kinase, and kinase substrates. J. Biol. Chem. 259:1984;10949-10955.
27. Stemmer P.M., Klee C.B. Dual calcium ion regulation of calcineurin by calmodulin and calcineurin B. Biochemistry. 33:1994;6859-6866.
28. 2+ binding and 1H NMR. J. Biol. Chem. 262:1987;10951-10954.
29. Ikura M., Clore G.M., Gronenborn A.M., Zhu G., Klee C.B., Bax A. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science. 256:1992;632-638.
30. Meador W.E., Means A.R., Quiocho F.A. Target enzyme recognition by calmodulin. 2.4 Å structure of a calmodulin-peptide complex Science. 257:1992;1251-1255.
31. Meador W.E., Means A.R., Quiocho F. Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structure. Science. 262:1993;1718-1721.
32. Yap K.L., Kim J., Truong K., Sherman M., Yuan T., Ikura M. Calmodulin Target Database. J. Struct. Funct. Genomics. 1:2000;8-14.
33. Ridgway E.B., Durham A.C.H. Oscillations of calcium ion concentrations in Physarum polycephalum. J. Cell Biol. 69:1976;223-226.
34. 2+ switch aligns the active site of calpain. Cell. 108:2002;649-660.
35. 15N NMR relaxation. Biochemistry. 32:1993;9832-9844.
36. 9k in the apo and singly and doubly calcium-loaded states. Proteins. 33:1998;265-284.
37. Gagné S.M., Tsuda S., Spyracopoulus L., Kay L.E., Sykes B.D. Backbone and methyl dynamics of the regulatory domain of tropoin C. anisotropic rotational diffusion and contribution of conformational entropy to calcium affinity J. Mol. Biol. 278:1998;667-686.
38. 2+-loaded human grancalcin. Acta Crystallogr. D Biol. Crystallogr. 57:2001;1843-1849.
39. Lollike K., Johnsen A.H., Durussel I., Borregaard N., Cox J.A. Biochemical characterization of the penta-EF-hand protein grancalcin and identification of L-plastin as a binding partner. J. Biol. Chem. 276:2001;17762-17769.
40. Borregaard N., Kjeldsen L., Lollike K., Sengelov H. Ca(2+)-dependent translocation of cytosolic proteins to isolated granule subpopulations and plasma membrane from human neutrophils. FEBS Lett. 304:1992;195-197.
41. Lollike K., Sorensen O., Bundgaard J.R., Segal A.W., Boyhan A., Borregaard N. An ELISA for grancalcin, a novel cytosolic calcium-binding protein present in leukocytes. J. Immunol. Methods. 185:1995;1-8.
42. Wilce M.C., Dooley D.M., Freeman H.C., Guss J.M., Matsunami H., McIntire W.S., Ruggiero C.E., Tanizawa K., Yamaguchi H. Crystal structures of the copper-containing amine oxidase from Arthrobacter globiformis in the holo and apo forms. implications for the biogenesis of topaquinone Biochemistry. 36:1997;16116-16133.
43. Otwinowski Z. Isomorphous replacement and anomalous scattering. Sawyer L., Isaacs N., Bailey S. Proceedings of the CCP4 Study Weekend. Data Collection and Processing:1993;SERC Daresbury Laboratory, Warrington, UK. 55-62.pp.
44. CCP4 The CCP4 (Collaborative Computational Project 4) suite. programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50:1994;760-763.
45. Jones A.T., Zou J.-Y., Cowtan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and for locating erros in these model. Acta Crystallogr. A. 47:1991;110-119.
46. Brünger A.T. X-PLOR Version 3.1. A System for X-Ray Crystallography and NMR:1992;Yale University Press, New Haven, CT.
47. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography and NMR system. a new software system for macromolecular structure determination Acta Crystallogr. D Biol Crystallogr. 54:1998;905-921.
48. Navaza J. AMoRe. an automated package for molecular replacement Acta Crystallogr. A. 50:1994;157-163.