Conserved residues in the mechanism of the E. coli class II FBP-aldolase

Journal of Molecular Biology

Volumn 285, Issue 2, 1999, Pages 843-855

  Plater, A R ^a   Zgiby, S M ^a   Thomson, G J ^a   Qamar, S ^a   Wharton, C W ^b   Berry, A ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Aldolases; Enzyme mechanism; Fourier transform infrared spectroscopy; Fructose 1,6 bisphosphate; Protein engineering

Indexed keywords

ASPARAGINE; ASPARTIC ACID; CARBONYL DERIVATIVE; DIHYDROXYACETONE PHOSPHATE; FERRICYANIDE; FRUCTOSE 1,6 BISPHOSPHATE; FRUCTOSE BISPHOSPHATE ALDOLASE; GLYCERALDEHYDE 3 PHOSPHATE; SCHIFF BASE;

ARTICLE; CATALYSIS; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; FELIS CATUS; NEGIBACTERIA;

EID: 0033556284     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2376     Document Type: Article

References (48)

1. Bacon D., Anderson W. F. A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 5:1988;219-220.
2. Barbas C. F., Heine A., Zhong G. F., Hoffmann T., Gramatikova S., Bjornestedt R., List B., Anderson J., Stura E. A., Wilson I. A., Lerner R. A. Immune versus natural selection: antibody aldolases with enzymic rates but broader scope. Science. 278:1997;2085-2092.
3. Belasco J. G., Knowles J. R. Direct observation of substrate distortion by triose phosphate isomerase using Fourier transform infra-red spectroscopy. Biochemistry. 19:1980;472-477.
4. Belasco J. G., Knowles J. R. Polarization of substrate carbonyl groups by yeast aldolase: investigation by Fourier transform infrared spectroscopy. Biochemistry. 22:1983;122-129.
5. Berry A., Marshall K. E. Identification of zinc-binding ligands in the Class II fructose-1,6-bisphosphate aldolase of E. coli. FEBS Letters. 318:1993;11-16.
6. Blom N. S., Sygusch J. Product binding and role of the C-terminal region in class I D-fructose 1,6-bisphosphate aldolase. Nature Struct. Biol. 4:1997;36-39.
7. Blom N. S., Tetreault S., Coulombe R., Sygusch J. Novel active site in Escherichia coli fructose-1,6-bisphosphate aldolase. Nature Struct. Biol. 3:1996;856-862.
8. Bradford M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:1976;248-254.
9. Collins K. D. An activated intermediate analogue. The use of phosphoglycolohydroxamate as a stable analogue of a transiently occurring dihydroxyacetone phosphate-derived enolate in enzymatic catalysis. J. Biol. Chem. 249:1974;136-142.
10. Cooper S. J., Leonard G. A., McSweeney S. M., Thompson A. W., Naismith J. H., Qamar S., Plater A., Berry A., Hunter W. N. The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding site embedded in a familiar fold. Structure. 4:1996;1303-1315.
11. Davenport R. C., Bash P. A., Seaton B. A., Karplus M., Petsko G. A., Ringe D. Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway. Biochemistry. 30:1991;5821-5826.
12. Desai, S. Y. 1997, Type II fructose-1,6-bisphosphate aldolase from Bacillus stearothermophilus. PhD thesis, University of Exeter.
13. Dreyer M. K., Schulz G. E. The spatial structure of the Class II L -fuculose-1-phosphate aldolase from Escherichia coli. J. Mol. Biol. 231:1993;549-553.
14. Dreyer M. K., Schulz G. E. Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. J. Mol. Biol. 259:1996;458-466.
15. Fessner W. Enzyme mediated C-C bond formation. Curr. Opin. Chem. Biol. 2:1998;85-97.
16. Fessner W. D., Schneider A., Held H., Sinerius G., Walter C., Hixon M., Schloss J. V. The mechanism of Class II, metal-dependent aldolases. Angew. Chem. Int. Ed. Engl. 35:1996;2219-2221.
17. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Bult C. J., Kerlavage A. R., Sutton G., Kelley J. M., Fritchman J. L., Weidman J. F., Small K. V., Sandusky M., Fuhrmann J. et al. The minimal gene complement of Mycoplasma genitalium. Science. 270:1995;397-403.
18. Gamblin S. J., Cooper B., Millar J. R., Davies G. J., Littlechild J. A., Watson H. C. The crystal structure of human muscle aldolase at 3. 0 Å resolution. FEBS Letters. 262:1990;282-286.
19. Gamblin S. J., Davies G. J., Grimes J. M., Jackson R. M., Littlechild J. A., Watson H. C. Activity and specificity of human aldolases. J. Mol. Biol. 219:1991;573-576.
20. Harris C. E., Kobes R. D., Teller D. C., Rutter W. J. The molecular characteristics of yeast aldolase. Biochemistry. 8:1969;2442-2454.
21. Healy M. J., Christen P. Mechanistic probes for enzymic reactions. Oxidation-reduction indicators as oxidants of intermediary carbanions (studies with aldolase, aspartate aminotransferase, pyruvate decarboxylase and 6-phosphogluconate dehydrogenase). Biochemistry. 12:1973;35-40.
22. Hester G., Brennerholzach O., Rossi F. A., Struckdonatz M., Winterhalter K. H., Smit J. D. G., Piontek K. The crystal structure of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster at 2.5 Å resolution. FEBS Letters. 292:1991;237-242.
23. Hill H. A., Lobb R. R., Sharp S. L., Stokes A. M., Harris J. I., Jack R. S. Metal-replacement studies in Bacillus stearothermophilus aldolase and a comparison of the mechanisms of Class I and Class II aldolases. Biochem. J. 153:1976;551-560.
24. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B. C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucl. Acid Res. 24:1996;4420-4449.
25. Horecker B. L., Tsolas O., Lai C. Y. Aldolases. The Enzymes. 1972;Academic Press, New York. p. 213-258.
26. Kadonaga J. T., Knowles J. R. Role of mono- and divalent metal cations in the catalysis by yeast aldolase. Biochemistry. 22:1983;130-136.
27. Kim H., Certa U., Dobeli H., Jakob P., Hol W. G. J. Crystal structure of fructose-1,6-bisphosphate aldolase from the human malaria parasite Plasmodium falciparum. Biochemistry. 37:1998;4388-4396.
28. Kobes R. D., Simpson R. T., Vallee B. L., Rutter W. J. A functional role of metal ions in a Class II aldolase. Biochemistry. 8:1969;585-588.
29. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
30. Merritt E. A., Murphy M. E. P. Raster3D version 2. 0 - A program for photrealistic molecular graphics. Acta Crystallog. sect. D. 50:1994;869-873.
31. Midelfort C. F., Gupta R. K., Rose I. A. Fructose 1,6-bisphosphate: isomeric composition, kinetics and substrate specificity for the aldolases. Biochemistry. 15:1976;2178-2185.
32. Morris A. J., Tolan D. R. Site-directed mutagenesis identifies aspartate-33 as a previously unidentified critical residue in the catalytic mechanism of rabbit aldolase A. J. Biol. Chem. 268:1993;1095-1100.
33. Qamar S., Marsh K. L., Berry A. Identification of arginine 331 as an important active site residue in the Class II fructose-1,6-bisphosphate aldolase ofE. coli. Protein Sci. 5:1996;154-161.
34. Reikofski Y., Tao B. Y. Polymerase chain reaction (PCR) techniques for site-directed mutagenesis. Biotech. Advan. 10:1992;535-547.
35. Richards O. C., Rutter W. J. Comparative properties of yeast and muscle aldolase. J. Biol. Chem. 236:1961a;3185-3192.
36. Richards O. C., Rutter W. J. Preparation and properties of yeast aldolase. J. Biol. Chem. 236:1961b;3177-3184.
37. Rose I. A., O'Connell E. L., Mehler A. H. Mechanism of the aldolase reaction. J. Biol. Chem. 240:1965;1758-1765.
38. Rutter W. J. Evolution of aldolase. Fed. Proc. Fed. Am. Soc. Exp. Biol. 23:1964;1248-1257.
39. Smith G. M., Mildvan A. S., Harper E. T. Nuclear relaxation studies of the interaction of substrates with a metalloaldolase from yeast. Biochemistry. 19:1980;1248-1255.
40. Stribling D., Perham R. N. Purification and characterisation of two fructose diphosphate aldolases from Escherichia coli (Crooke's strain). Biochem. J. 131:1973;833-841.
41. Sygusch J., Beaudry D., Allaire M. Molecular architecture of rabbit skeletal muscle aldolase at 2.7 Å resolution. Proc. Natl Acad. Sci. USA. 84:1987;7846-7850.
42. Taylor J. W., Ott J., Eckstein F. The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate modified DNA. Nucl. Acid Res. 13:1985;8765-8785.
43. Thomson G. J., Howlett G. J., Ashcroft A. E., Berry A. The dhn A gene of Escherichia coli encodes a Class I fructose bisphosphate aldolase. Biochem. J. 331:1998;437-445.
44. Trentham D. R., McMurray C. H., Pogson C. I. The active chemical state of D-glyceraldehyde 3-phosphate in its reactions with D-glyceraldehyde-3-phosphate dehydrogenase, aldolase and triose phosphate isomerase. Biochem. J. 114:1969;19-24.
45. Wagner J., Lerner R. A., Barbas C. F. Efficient aldolase catalytic antibodies that use the enamine mechanism of natural enzymes. Science. 270:1995;1797-1800.
46. Webb M. R., Standring D. N., Knowles J. R. Phosphorus-31 nuclear magnetic resonance of dihydroxyacetone phosphate in the presence of triose phosphate isomerase. The question of non-productive binding of the substrate hydrate. Biochemistry. 16:1977;2738-2741.
47. Wong C.-H., Whitesides G. M. Enzymes in Synthetic Organic Chemistry. 1994;Pergamon, Oxford.
48. Yoshida K., Sano H., Miwa Y., Ogasawara N., Fujita Y. Cloning and nucleotide sequencing of a 15kb region of the Bacillus subtilis genome containing the iol operon. Microbiology. 140:1994;2289-2298.