Calcium supports loop closure but not catalysis in Rubisco

Journal of Molecular Biology

Volumn 334, Issue 1, 2003, Pages 65-73

  Karkehabadi, Saeid ^a   Taylor, Thomas C ^a   Andersson, Inger ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Calcium activation; Ligand complexes; Loop movements; Merohedral twinning; Ribulose 1,5 bisphosphate carboxylase oxygenase

Indexed keywords

2 CARBOXY DEXTRO ARABINITOL 1,5 BISPHOSPHATE; CALCIUM ION; CARBAMIC ACID; LEWIS ACID; PHOSPHATE; RIBULOSEBISPHOSPHATE CARBOXYLASE; UNCLASSIFIED DRUG;

ARTICLE; CARBAMOYLATION; CATALYSIS; CATALYST; ENZYME ASSAY; ENZYME STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTON TRANSPORT; REDUCTION;

HUMULUS;

EID: 0142195731     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.09.025     Document Type: Article

References (47)

1. Hartman F.C., Harpel M.C. Structure, function, regulation, and assembly of D-ribulose-1,5-bisphosphate carboxylase oxygenase. Annu. Rev. Biochem. 63:1994;197-234.
2. Cleland W.W., Andrews T.J., Gutteridge S., Hartman F.C., Lorimer G. Mechanism of Rubisco: the carbamate as a general base. Chem. Rev. 98:1998;549-561.
3. Spreitzer R.J. Questions about the complexity of chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase. Photosynth. Res. 60:1999;29-42.
4. Spreitzer R.J., Salvucci M.E. Rubisco: structure, regulatory interactions, and possibilities for a better enzyme. Annu. Rev. Plant Biol. 53:2002;449-475.
5. Weissbach A., Horecker B.L., Hurwitz J. The enzymatic formation of phosphoglyceric acid from ribulose diphosphate and carbon dioxide. J. Biol. Chem. 218:1956;795-810.
6. Wishnick M., Lane D., Scrutton M.C. The interaction of metal ions with ribulose 1,5-diphosphate carboxylase from spinach. J. Biol. Chem. 245:1970;4939-4947.
7. - into a cobalt(III)-enzyme complex. Biochemistry. 18:1979;4453-4458.
8. Taylor T.C., Andersson I. The structure of the complex between Rubisco and its natural substrate ribulose 1,5-bisphosphate. J. Mol. Biol. 265:1997;432-444.
9. Schneider G., Lindqvist Y., Brändén C.-I., Lorimer G. Three-dimensional structure of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum at 2.9 Å resolution. EMBO J. 5:1986;3409-3415.
10. Kitano K., Maeda N., Fukui T., Atomi H., Imanaka T., Miki K. Crystal structure of a novel-type archaeal Rubisco with pentagonal structure. Structure. 9:2001;473-481.
11. Andrews T.J. Catalysis by cyanobacterial ribulose-bisphosphate carboxylase large subunits in the complete absence of small subunits. J. Biol. Chem. 263:1988;12213-12219.
12. Andersson I., Taylor T.C. Structural framework for catalysis and activation in ribulose-1,5-bisphosphate carboxylase/oxygenase. Arch. Biochem. Biophys. 414:2003;130-140.
13. Schreuder H.A., Knight S., Curmi P.M.G., Andersson I., Cascio D., Brändén C.-I., Eisenberg D. Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form. Proc. Natl Acad. Sci. USA. 90:1993;9968-9972.
14. Taylor T.C., Andersson I. Structural transitions during activation and ligand binding in hexadecameric Rubisco inferred from the crystal structure of the activated unliganded spinach enzyme. Nature Struct. Biol. 3:1996;95-101.
15. Duff A.P., Andrews T.J., Curmi P.M.G. The transition between the open and closed states of Rubisco is triggered by the inter-phosphate distance of the bound bisphosphate. J. Mol. Biol. 298:2000;903-916.
16. Andersson I., Knight S., Schneider G., Lindqvist Y., Lundqvist T., Brändén C.-I., Lorimer G.H. Structure of the active site of ribulose-bisphhosphate carboxylase. Nature. 337:1989;229-234.
17. Newman J., Brändén C.-I., Jones T.A. The X-ray structure of Synechococcus ribulose-1,5-bisphosphate carboxylase/oxygenase-activated quaternary complex at 2.2 Å resolution. Acta Crystallog. sect. D. 49:1993;548-560.
18. Andersson I. Large structures at high resolution: the 1.6 Å crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate. J. Mol. Biol. 259:1996;160-174.
19. Sugawara H., Yamamoto H., Shibata N., Inoue T., Okada S., Miyake C., et al. Crystal structure of carboxylase reaction-oriented ribulose-1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita. J. Biol. Chem. 274:1999;15655-15661.
20. Taylor T.C., Backlund A., Spreitzer R.J., Björhall K., Andersson I. First crystal structure of Rubisco from a green alga-Chlamydomonas reinhardtii. J. Biol. Chem. 276:2001;48159-48164.
21. Mizohata E., Matsumura H., Okano Y., Kumei M., Takuma H., Onodera J., et al. Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate. J. Mol. Biol. 316:2002;679-691.
22. Taylor T.C., Andersson I. Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. Biochemistry. 36:1997;4041-4046.
23. Hajdu J., Andersson I. Fast X-ray crystallography and time-resolved structures. Annu. Rev. Biophys. Biomol. Struct. 22:1993;467-498.
24. Yeates T.O. Detwinning and overcoming crystal twinning. Methods Enzymol. 276:1997;344-358.
25. Terwisscha van Scheltinga A.C., Valegård K., Ramaswamy S., Hajdu J., Andersson I. Multiple isomorphous replacement with merohedral twins: structure determination of deacetoxycephalosporin C synthase. Acta Crystallog. sect. D. 57:2001;1776-1785.
26. Rees D.C. The influence of twinning by merohedry on intensity statistics. Acta Crystallog. sect. A. 36:1980;578-581.
27. 2+ on activation and catalysis of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. EMBO J. 2:1983;2363-2367.
28. Andersson I., Brändén C.-I. Large single crystals of spinach 1,5-bisphosphate carboxylase/oxygenase suitable for X-ray studies. J. Mol. Biol. 172:1984;363-366.
29. Pal G.P., Jakob R., Hahn U., Bowien B., Saenger W. Single and twinned crystals of ribulose-1,5-diphosphate carboxylase-oxygenase from Alcaligenes eutrophus. J. Biol. Chem. 260:1985;10768-10770.
30. Pickersgill R.W. One-dimensional disorder in spinach ribulose bisphosphate carboxylase crystals. Acta Crystallog. sect. A. 43:1987;502-506.
31. Yang F., Dauter Z., Wlodawer A. Effects of crystal twinning on the ability to solve a macromolecular structure using multiwavelength anomalous diffraction. Acta Crystallog. sect. D. 56:2000;959-964.
32. Bailey S. The CCP4 suite-programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
33. Fraústo da Silva J.J.R., Williams R.J.P. The Biological Chemistry of the Elements. The Inorganic Chemistry of Life. 1991;Oxford University Press, Oxford.
34. Harding M.M. The geometry of metal-ligand interactions relevant to proteins. Acta Crystallog. sect. D. 55:1999;1432-1443.
35. 2 fixation by Rubisco: computational dissection of the key steps of carboxylation, hydration, and C-C bond cleavage. J. Am. Chem. Soc. 123:2001;10821-10829.
36. Knight S., Andersson I., Brändén C.-I. Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 Å resolution: subunit interactions and the active site. J. Mol. Biol. 215:1990;113-160.
37. Newman J., Gutteridge S. The X-ray structure of Synechococcus ribulose-bisphosphate carboxylase oxygenase-activated quaternary complex at 2.2-Å resolution. J. Biol. Chem. 268:1993;25876-25886.
38. Curmi P.M.G., Cascio D., Sweet R.M., Eisenberg D., Schreuder H.A. Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0 Å resolution. J. Biol. Chem. 267:1992;16980-16989.
39. Andersson I., Tjäder A.-C., Cedergren-Zeppezauer E., Brändén C.-I. Preliminary X-ray studies of spinach ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with activator and a transition state analogue. J. Biol. Chem. 258:1983;14088-14090.
40. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
41. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D. 53:1997;240-255.
42. Taylor T.C., Fothergill M.D., Andersson I. A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate. J. Biol. Chem. 271:1997;32894-32899.
43. Perrakis A., Sixma T.K., Wilson K.S., Lamzin V.S. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. Acta Crystallog. sect. D. 53:1997;448-455.
44. Jones T.A., Bergdoll M., Kjeldgaard M. O: a macromolecule modelling environment. Bugg C., Ealick S. Crystallographic and Modeling Methods (in Molecular Design). 1990;189-190 Springer, New York.
45. Esnouf R.M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallog. sect. D. 55:1999;938-940.
46. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein. J. Appl. Crystallog. 24:1991;946-950.
47. Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.