Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain

Proteins: Structure, Function and Genetics

Volumn 73, Issue 1, 2008, Pages 43-52

  Aragão, Karoline Saboia ^a   Satre, Michel ^b   Imberty, Anne ^a   Varrot, Annabelle ^a  

^a UNIV GRENOBLE ALPES   (France)

^b CEA GRENOBLE   (France)

Author keywords

Discoidin domain; Galactose binding domain; H type lectin

Indexed keywords

CARBOHYDRATE; DISCOIDIN; DISCOIDIN 2; LECTIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DICTYOSTELIUM DISCOIDEUM; ENTHALPY; HYDROGEN BOND; MICROCALORIMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; WILD TYPE;

ACETYLGALACTOSAMINE; ANIMALS; BINDING SITES; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DICTYOSTELIUM; LECTINS; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; RECOMBINANT PROTEINS;

AMOEBA (GENUS); DICTYOSTELIUM; DICTYOSTELIUM DISCOIDEUM; EUKARYOTA; INVERTEBRATA;

EID: 50849141733     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22038     Document Type: Article

References (49)

1. Firtel RA, Meili R. Dictyostelium: a model for regulated cell movement during morphogenesis. Curr Opin Genet Dev 2000;10:421-427.
2. Steinert M, Heuner K. Dictyostelium as host model for pathogenesis. Cell Microbiol 2005;7:307-314.
3. Williams RS, Boeckeler K, Graf R, Muller-Taubenberger A, Li Z, Isberg RR, Wessels D, Soll DR, Alexander H, Alexander S. Towards a molecular understanding of human diseases using Dictyostelium discoideum. Trends Mol Med 2006;12:415-424.
4. Willard SS, Devreotes PN. Signaling pathways mediating Chemotaxis in the social amoeba, Dictyostelium discoideum. Eur J Cell Biol 2006; 85:897-904.
5. Bonner JT. Aggregation and differentiation in the cellular slime molds. Annu Rev Microbiol 1971;25:75-92.
6. Frazier WA, Rosen SD, Reitherman RW, Barondes SH. Purification and comparison of two developmentally regulated lectins from Dictyostelium discoideum. Discoidin I and II. J Biol Chem 1975;250: 7714-7721.
7. Berger EA, Armant DR. Discoidins I and II: common and unique regions on two lectins implicated in cell-cell cohesion in Dictyostelium discoideum. Proc Natl Acad Sci USA 1982;79:2162-2166.
8. Cooper DN, Lee SC, Barondes SH. Discoidin-binding polysaccharide from Dictyostelium discoideum. J Biol Chem 1983;258:8745-8750.
9. Barondes SH, Cooper DN, Haywood-Reid PL. Discoidin I and discoidin II are localized differently in developing Dictyostelium discoideum. J Cell Biol 1983;96:291-296.
10. Baumgartner S, Hofmann K, Chiquet-Ehrismann R, Bucher P. The discoidin domain family revisited: new members from prokaryotes and a homology-based fold prediction. Protein Sci 1998;7:1626-1631.
11. Kiedzierska A, Smietana K, Czepczynska H, Otlewski J. Structural similarities and functional diversity of eukaryotic discoidin-like domains. Biochim Biophys Acta 2007;1774:1069-1078.
12. Jimbo M, Koike K, Sakai R, Muramoto K, Kamiya H. Cloning and characterization of a lectin from the octocoral Sinularia lochmodes. Biochem Biophys Res Commun 2005;330:157-162.
13. Sanchez JF, Lescar J, Chazalet V, Audfray A, Gagnon J, Alvarez R, Breton C, Imberty A, Mitchell EP. Biochemical and structural analysis of Helix pomatia agglutinin. A hexameric lectin with a novel fold. J Biol Chem 2006;281:20171-20180.
14. Springer WR, Cooper DN, Barondes SH. Discoidin I is implicated in cell-substratum attachment and ordered cell migration of Dictyostelium discoideum and resembles fibronectin. Cell 1984;39:557-564.
15. Gabius HJ, Springer WR, Barondes SH. Receptor for the cell binding site of discoidin I. Cell 1985;42:449-456.
16. Simpson DL, Rosen SD, Barondes SH. Discoidin, a developmentally regulated carbohydrate-binding protein from Dictyostelium discoideum. Purification and characterization. Biochemistry 1974;13: 3487-3493.
17. Kapust RB, Tozser J, Fox JD, Anderson DE, Cherry S, Copeland TD, Waugh DS. Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng 2001;14:993-1000.
18. Wiseman T, Williston S, Brandts JF, Lin LN. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal Biochem 1989;179:131-137.
19. Leslie AGW. Recent changes to the MOSFLM package for processing film and image plate data. Jnt CCP4/ESF-EACMB Newsletter on Protein Crystallography, 1992. p 26.
20. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Cryst 1993;26:795-800.
21. Collaborative computational project number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
22. Vonrhein C, Blanc E, Roversi P, Bricogne G. Automated structure solution with autoSHARP. Methods Mol Biol 2006;364:215-230.
23. Navaza J, Saludjian P. AMoRe: an automated molecular replacement program package. In: C W Carter J, Sweet RM, editors. Methods Enzymol. Volume 276. London: Academic Press; 1997. pp 581-594.
24. McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ. Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr 2005;61:458-464.
25. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997;53:240-255.
26. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004;60:2126-2132.
27. Loomis WF, Shaulsky G, Wang N. Histidine kinases in signal transduction pathways of eukaryotes. J Cell Sci 1997;110:1141-1145.
28. Thomason PA, Sawai S, Stock JB, Cox EC. The histidine kinase homologue DhkK/Sombrero controls morphogenesis in Dictyostelium. Dev Biol 2006;292:358-370.
29. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;24:536-540.
30. Potterton E, Briggs P, Turkenburg M, Dodson E. A graphical user interface to the CCP4 program suite. Acta Crystallogr D Biol Crystallogr 2003;59:1131-1137.
31. Ichikawa O, Osawa M, Nishida N, Goshima N, Nomura N, Shimada I. Structural basis of the collagen-binding mode of discoidin domain receptor 2. EMBO J 2007;26:4168-4176.
32. Lee CC, Kreusch A, McMullan D, Ng K, Spraggon G. Crystal structure of the human neuropilin-1 b1 domain. Structure 2003;11:99-108.
33. Lin L, Huai Q, Huang M, Furie B, Furie BC. Crystal structure of the bovine lactadherin C2 domain, a membrane binding motif, shows similarity to the C2 domains of factor V and factor VIII. J Mol Biol 2007;371:717-724.
34. Macedo-Ribeiro S, Bode W, Huber R, Quinn-Allen MA, Kim SW, Ortel TL, Bourenkov GP, Bartunik HD, Stubbs MT, Kane WH, Fuentes-Prior P. Crystal structures of the membrane-binding C2 domain of human coagulation factor V. Nature 1999;402:434-439.
35. Pratt KP, Shen BW, Takeshima K, Davie EW, Fujikawa K, Stoddard BL. Structure of the C2 domain of human factor VIII at 1.5 A resolution. Nature 1999;402:439-442.
36. Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 2004;60:2256-2268.
37. Fuentes-Prior P, Fujikawa K, Pratt KP. New insights into binding interfaces of coagulation factors V and VIII and their homologues lessons from high resolution crystal structures. Curr Protein Pept Sci 2002;3:313-339.
38. Bianchet MA, Odom EW, Vasta GR, Amzel LM. A novel fucose recognition fold involved in innate immunity. Nature Struct Biol 2002;9:628-634.
39. Boraston AB, Wang D, Burke RD. Blood group antigen recognition by a Streptococcus pneumoniae virulence factor. J Biol Chem 2006; 281:35263-35271.
40. Gaskell A, Crennell S, Taylor G. The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll. Structure 1995;3:1197-1205.
41. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Nature 1991;350:87-90.
42. Wendt KS, Vodermaier HC, Jacob U, Gieffers C, Gmachl M, Peters JM, Huber R, Sondermann P. Crystal structure of the APC10/ DOC1 subunit of the human anaphase-promoting complex. Nature Struct Biol 2001;8:784-788.
43. Dam TK, Brewer CF. Thermodynamic studies of lectin-carbohydrate interactions by isothermal titration calorimetry. Chem Rev 2002;102: 387-429.
44. Lescar J, Sanchez JF, Audfray A, Coll JL, Breton C, Mitchell EP, Imberty A. Structural basis for recognition of breast and colon cancer epitopes Tn antigen and Forssman disaccharide by Helix pomatia lectin. Glycobiology 2007;17:1077-1083.
45. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-138.
46. Lucas RW, Larson SB, McPherson A. The crystallographic structure of brome mosaic virus. J Mol Biol 2002;317:95-108.
47. Zhang L, Koay M, Maher MJ, Xiao Z, Wedd AG. Intermolecular transfer of copper ions from the CopC protein of Pseudomonas syringae. Crystal structures of fully loaded Cu(I)Cu(II) forms. J Am Chem Soc 2006;128:5834-5850.
48. Gouet P, Courcelle E, Stuart DI, Metoz F. ESPript: multiple sequence alignments in postscript. Bioinformatics 1999;15:305-308.
49. Sharon N. Protein-carbohydrate interactions - at the art of biochemistry. The Biochemist 2006; pp 1-5.