Structural insights into the substrate binding and stereoselectivity of giardia fructose-1,6-bisphosphate aldolase

Biochemistry

Volumn 48, Issue 14, 2009, Pages 3186-3196

  Galkin, Andrey ^a   Li, Zhimin ^b   Li, Ling ^b   Kulakova, Liudmila ^a   Pal, Lipika R ^a   Dunaway Mariano, Debra ^b   Herzberg, Osnat ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITES; ALANINE RESIDUES; ALDOLASE; ASPARTATE RESIDUES; ASPARTIC ACIDS; BISPHOSPHATE; CARBOXYL GROUPS; CARBOXYLATE GROUPS; CARBOXYLIC GROUPS; CATALYTIC APPARATUS; CATALYTIC MECHANISMS; CO-PLANARITY; CONFORMATIONAL TRANSITIONS; D FRUCTOSE; D-TAGATOSE; DIHYDROXYACETONE PHOSPHATES; GIARDIA; GIARDIA LAMBLIA; HYDROXYL GROUPS; SEQUENCE ANALYSIS; SIDE CHAINS; STRUCTURAL INSIGHTS; SUBSTRATE BINDINGS; SUBSTRATE DISCRIMINATIONS; SUBSTRATE SPECIFICITIES; TAGATOSE; UNBOUND STATE; WILD TYPES;

CARBOXYLATION; COORDINATION REACTIONS; ENZYMES; FRUCTOSE; ORGANIC ACIDS; PROTON TRANSFER; QUANTUM CHEMISTRY; STEREOSELECTIVITY; SUBSTRATES;

ZINC;

ALANINE; ASPARTIC ACID; CARBOXYL GROUP; CARBOXYLIC ACID DERIVATIVE; DEXTRO TAGATOSE 1,6 BISPHOSPHATE; DIHYDROXYACETONE PHOSPHATE; FRUCTOSE BISPHOSPHATE ALDOLASE; GLYCERALDEHYDE 3 PHOSPHATE; HYDROXAMIC ACID DERIVATIVE; HYDROXYL GROUP; PHOSPHOGLYCOLOHYDROXAMATE; TAGATOSE; UNCLASSIFIED DRUG; ZINC;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; COMPARATIVE STUDY; COMPETITIVE INHIBITION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; GIARDIA LAMBLIA; NONHUMAN; POLARIZATION; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN STRUCTURE; PROTON TRANSPORT; STEREOCHEMISTRY; SUBSTITUTION REACTION; WILD TYPE;

ANIMALS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; FRUCTOSE-BISPHOSPHATE ALDOLASE; FRUCTOSEDIPHOSPHATES; GIARDIA; HEXOSEDIPHOSPHATES; KINETICS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTOZOAN PROTEINS; STEREOISOMERISM; SUBSTRATE SPECIFICITY; ZINC;

GIARDIA; GIARDIA INTESTINALIS;

EID: 65249126756     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9001166     Document Type: Article

References (27)

1. Kobes, R. D., Simpson, R. T., Vallee, R. L., and Rutter, W. J. (1969) A functional role of metal ions in a class II aldolase. Biochemistry 8, 585-588.
2. Rutter, W. J. (1964) Evolution of Aldolase. Fed. Proc. 23, 1248-1257.
3. Blom, N. S., Tetreault, S., Coulombe, R., and Sygusch, J. (1996) Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase. Nat. Struct. Biol. 3, 856-862.
4. Cooper, S. J., Leonard, G. A., McSweeney, S. M., Thompson, A. W, Naismith, J. H., Qamar, S., Plater, A., Berry, A., and Hunter, W. N. (1996) The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold. Structure 4, 1303-1315.
5. Hall, D. R., Leonard, G. A., Reed, C. D., Watt, C. I., Berry, A., and Hunter, W. N. (1999) The crystal structure of Escherichia coli class II fructose-1,6-bisphosphate aldolase in complex with phos-phoglycolohydroxamate reveals details of mechanism and specificity. J. Mol. Biol. 287, 383-394.
6. Hall, D. R., Bond, C. S., Leonard, G. A., Watt, C. I., Berry, A., and Hunter, W.N. (2002) Structure of tagatose-1,6-bisphosphate aldolase. Insight into chiral discrimination, mechanism, and specificity of class II aldolases. J. Biol. Chem. 277, 22018-22024.
7. Plater, A. R., Zgiby, S. M., Thomson, G. J., Qamar, S., Wharton, C. W., and Berry, A. (1999) Conserved residues in the mechanism of the E. coli Class II FBP-aldolase. J. Mol. Biol. 285, 843-855.
8. Zgiby, S. M., Thomson, G. J., Qamar, S., and Berry, A. (2000) Exploring substrate binding and discrimination in fructose 1,6-bisphosphate and tagatose 1,6-bisphosphate aldolases. Eur. J. Biochem. 267, 1858-1868.
9. Zgiby, S., Plater, A. R., Bates, M. A., Thomson, G. J., and Berry, A. (2002) A functional role for a flexible loop containing Glu182 in the class II fructose-1,6-bisphosphate aldolase from Escherichia coli. J. Mol. Biol. 315, 131-140.
10. Galkin, A., Kulakova, L., Melamud, E., Li, L., Wu, C., Mariano, P., Dunaway-Mariano, D., Nash, T. E., and Herzberg, O. (2007) Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia. J. Biol. Chem. 282, 4859-4867.
11. Henze, K., Morrison, H. G., Sogin, M. L., and Muller, M. (1998) Sequence and phylogenetic position of a class II aldolase gene in the amitochondriate protist, Giardia lamblia. Gene 222, 163-168.
12. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C., and Read, R. J. (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr. D61, 458-464.
13. Jones, T. A. (2004) Interactive electron-density map interpretation: From INTER to O. Acta Crystallogr. 60, 2115-2125.
14. Brünger, 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., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. 54, 905-921.
15. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255.
16. Laskowski, R. A., and MacArthur, M. W. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
17. DeLano, W. L. (2002) The PyMOL User's Manual, DeLano Scientific, San Carlos, CA.
18. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254.
19. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
20. Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
21. Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004) WebLogo: A sequence logo generator. Genome Res. 14, 1188-1190.
22. Izard, T., and Sygusch, J. (2004) Induced fit movements and metal cofactor selectivity of class II aldolases: Structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase. J. Biol. Chem. 279, 11825-11833.
23. Midelfort, C. F., Gupta, R. K., and Rose, I. A. (1976) Fructose 1,6-bisphosphate: Isomeric composition, kinetics, and substrate specificity for the aldolases. Biochemistry 15, 2178-2185.
24. Qamar, S., Marsh, K., and Berry, A. (1996) Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli. Protein Sci. 5, 154-161.
25. Alberts, I. L., Nadassy, K., and Wodak, S. J. (1998) Analysis of zinc binding sites in protein crystal structures. Protein Sci. 7, 1700-1716.
26. Williams, G. J., Domann, S., Nelson, A., and Berry, A. (2003) Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolution. Proc. Natl. Acad. Sci. U.S.A. 100, 3143-3148.
27. Schneider, T. D., and Stephens, R. M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18, 6097-6100.