Bioinformatic tools uncover the C-terminal strand of Rubisco's large subunit as hot-spot for specificity-enhancing mutations

FEBS Letters

Volumn 581, Issue 4, 2007, Pages 741-748

  Burisch, C ^a   Wildner, G F ^a   Schlitter, J ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Rubisco; Sequence analysis; Simulation; Specificity; Targeted molecular dynamics; Time window hypothesis

Indexed keywords

RIBULOSEBISPHOSPHATE CARBOXYLASE;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; ENZYME SPECIFICITY; ENZYME SUBUNIT; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CONSERVED SEQUENCE; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; MUTATION; PROTEIN SUBUNITS; RIBULOSE-BISPHOSPHATE CARBOXYLASE; SEQUENCE ANALYSIS, PROTEIN; SUBSTRATE SPECIFICITY; SYNECHOCOCCUS;

EID: 33846828598     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.01.043     Document Type: Article

References (40)

1. Spreitzer R.J., and Salvucci M.E. Rubisco: structure, regulatory interactions, and possibilities for a better enzyme. Annu. Rev. Plant Biol. 53 (2002) 449-475
2. Kellogg E.A., and Juliano N.D. The structure and function of RuBisCO and their implications for systematic studies. Am. J. Bot. 84 (1997) 413-428
3. Wildner G.F., Schlitter J., and Muller M. Rubisco, an old challenge with new perspectives. Z. Naturforsch., C, J. Biosci. 51 (1996) 263-276
4. 2 specificity-determining factors for ribulose 1,5-bisphosphate carboxylase/oxygenase. Protein Eng. Des. Sel. 18 (2005) 589-596
5. Wildner F.G., Schlitter J., and Stutzel T. Phylogenetic analysis of the C-terminal sequence of rbcl. Plant Biol. 1 (1999) 656-664
6. 2 specificity of Rubisco on the carboxy-terminus of the large subunit at different temperatures. Photosynth. Res. 57 (1998) 71-79
7. Gutteridge S., Rhoades D., and Herrmann C. Site-specific mutations in a loop region of the C-terminal domain of the large subunit of ribulose bisphosphate carboxylase/oxygenase that influence substrate partitioning. J. Biol. Chem. 268 (1993) 7818-7824
8. Schlitter J., and Wildner G.F. The kinetics of conformation change as determinant of Rubisco's specificity. Photosynth. Res. 65 (2000) 7-13
9. 2 specificity factor for ribulose bisphosphate carboxylase/oxygenase. Photosynth. Res. 54 (1997) 127-134
10. Tcherkez G.G., Farquhar G.D., and Andrews T.J. Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized. Proc. Natl. Acad. Sci. USA 103 (2006) 7246-7251
11. Schlitter J., Engels M., Kruger P., Jacoby E., and Wollmer A. Targeted molecular-dynamics simulation of conformational change - application to the T-R transition in insulin. Mol. Simulat. 10 (1993) 291-308
12. Thompson J.D., Higgins D.G., and Gibson T.J. Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
13. van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J. GROMACS: fast, flexible, and free. J. Comput. Chem. 26 (2005) 1701-1718
14. van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hunenberger, P.H., Kruger, P., Mark, A.E., Scott, W.R.P. and Tironi, I.G. (1996) Biomolecular simulation: The GROMOS96 manual and user guide. BIOMOS, Zurich, Groningen.
15. Gutteridge S. The relative catalytic specificities of the large subunit core of Synechococcus ribulose bisphosphate carboxylase oxygenase. J. Biol. Chem. 266 (1991) 7359-7362
16. Roy H., and Andrews T.J. Rubisco: assembly and mechanism. In: Kennedy R. (Ed). Photosynthesis: Physiology and Metabolism Vol. 9 (2000), Kluwer Academic Publishers, Dordrecht 53-83
17. 2 by Rubisco. Biochemistry 37 (1998) 15414-15422
18. Schuttelkopf A.W., and van Aalten D.M.F. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. Sect. D - Biol. Crystallogr. 60 (2004) 1355-1363
19. Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8 (1990) 52-56
20. Bairoch A., Boeckmann B., Ferro S., and Gasteiger E. Swiss-Prot: juggling between evolution and stability. Brief. Bioinformat. 5 (2004) 39-55
21. Mizohata E., et al. Crystal structure of activated ribulose-l,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-l,5-bisphosphate. J. Mol. Biol. 316 (2002) 679-691
22. Schlitter J., Swegat W., and Mulders T. Distance-type reaction coordinates for modelling activated processes. J. Mol. Mod. 7 (2001) 171-177
23. Schlitter J., and Klahn M. A new concise expression for the free energy of a reaction coordinate. J. Chem. Phys. 118 (2003) 2057-2060
24. Parry M.A.J., Madgwick P.J., Parmar S., Cornelis M.J., and Keys A.J. Mutations in loop six of the large subunit of rubulose-l,5-bisphosphate carboxylase affect substrate specificity. Planta 81 (1992) 943-945
25. Read B.A., and Tabita F.R. High substrate specificity factor ribulose bisphosphate carboxylase/oxygenase from eukaryotic marine algae and properties of recombinant cyanobacterial rubisco containing "algal" residue modifications. Arch. Biochem. Biophys. 312 (1994) 210-218
26. Madgwick P.J., Parmar S., and Parry M.A.J. Effect of mutations of residue 340 in the large subunit polypeptide of Rubisco from Anacystis nidulans. Eur. J. Biochem. 253 (1998) 476-479
27. Bainbridge G., Madgwick P., Parmar S., Mitchell R., Paul M., Pitts J., Keys A.J., and Parry M.A.J. Engineering Rubisco to change its catalytic properties. J. Exp. Bot. 46 (1995) 1269-1276
28. Spreitzer R.J., and Satagopan S. Substitutions at the Asp-473 latch residue of Chlamydomonas ribulosebisphophate carboxylase/oxygenase cause decrease in carboxylation efficiency and CO2/O2 specificity. J. Biol. Chem. 279 (2004) 14240-14244
29. Portis Jr. A.R. Partial reduction in ribulose-1,5-bisphosphate carboxylase-oxygenase activity by carboxypeptidase A. Arch. Biochem. Biophys. 283 (1990) 397-400
30. Duff A.P., Andrews J., and 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
31. Cleland W.W., Andrews T.J., Gutteridge S., Hartman F.C., and Lorimer G.H. Mechanism of Rubisco: the carbamate as general base 98 (1998) 549-562
32. Jordan D.B., and Ogren W.L. Species variation in the specificity of ribulosebisphosphate carboxylase-oxygenase. Nature 291 (1981) 513-515
33. 2 specificity of ribulosebisphosphate carboxylase-oxygenase. Aust. J. Plant Physiol. 21 (1994) 449-461
34. Uemura K., Suzuki Y., Shikanai T., Wadano A., Jensen R.G., Chmara W., and Yokota A. A rapid and sensitive method for determination of relative specificity of RuBisCO from various species by anion-exchange chromatography. Plant Cell Physiol. 37 (1996) 325-331
35. Balaguer L., Afif D., Dizengremel P., and Dreyer E. Specificity factor of ribulose bisphosphate carboxylase/oxygenase of Quercus robur. Plant Physiol. Biochem. 34 (1996) 879-883
36. Galmes J., et al. Rubisco specificity factor tends to be larger in plant species from drier habitats and in species with persistent leaves. Plant Cell Environ. 28 (2005) 571-579
37. Hayashi N.R., Oguni A., Yaguchi T., Chung S.-Y., Nishihara H., Kodama T., and Igarashi Y. Different properties of gene products of three sets ribulose 1,5-bisphosphate carboxylase/oxygenase from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. J. Ferment. Bioeng. 85 (1998) 150-155
38. Tabita F.R. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynth. Res. 60 (1999) 1-28
39. Keys A.J. Rubisco: its role in photorespiration. Phil. Trans. Roy. Soc. Lond. B 313 (1986) 325-336
40. Parry M.A.J., Keys A.J., and Gutteridge S. Variation in the specificity factor of C-3 higher plant Rubiscos determined by the total consumption of ribulose bisphosphate. J. Exp. Bot. 40 (1989) 317-320