Structural Basis for Catalysis of a Tetrameric Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

Journal of Molecular Biology

Volumn 386, Issue 4, 2009, Pages 1038-1053

  Pegan, Scott D ^a   Rukseree, Kamolchanok ^a,b   Franzblau, Scott G ^a   Mesecar, Andrew D ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

Author keywords

aldol condensation; class II fructose 1,6 bisphosphate aldolase; dihydroxyacetone; glyceraldehyde 3 phosphate; Mycobacterium tuberculosis

Indexed keywords

BACTERIAL ENZYME; DIHYDROXYACETONE; DIHYDROXYACETONE PHOSPHATE; FRUCTOSE BISPHOSPHATASE; FRUCTOSE BISPHOSPHATE ALDOLASE; GLYCERALDEHYDE 3 PHOSPHATE; TETRAMER;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; ENZYME ASSAY; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; HYDROLYSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN QUATERNARY STRUCTURE; REACTION ANALYSIS; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

MYCOBACTERIUM TUBERCULOSIS;

EID: 60149098165     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.01.003     Document Type: Article

References (37)

1. World Health Organization. (2008). Global Tuberculosis Control 2008: Surveillance, Planning, Financing. pp. 1-5, Geneva, Switzerland.
2. World Health Organization. (2008). 2007-2008 XDR & MDR Tuberculosis Global Response Plan. pp. 1-2, Geneva, Switzerland.
3. Rutter W.J. Evolution of aldolase. Fed. Proc. 23 (1964) 1248-1257
4. Ramsaywak P.C., Labbe G., Siemann S., Dmitrienko G.I., and Guillemette J.G. Molecular cloning, expression, purification, and characterization of fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis-a novel class II A tetramer. Protein Expression Purif. 37 (2004) 220-228
5. Izard T., and Sygusch J. Induced fit movements and metal cofactor selectivity of class II aldolases: structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase. J. Biol. Chem. 279 (2004) 11825-11833
6. Galkin A., Kulakova L., Melamud E., Li L., Wu C., Mariano P., et al. Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia. J. Biol. Chem. 282 (2007) 4859-4867
7. Marsh J.J., and Lebherz H.G. Fructose-bisphosphate aldolases: an evolutionary history. Trends Biochem. Sci. 17 (1992) 110-113
8. Gerdes S.Y., Scholle M.D., Campbell J.W., Balazsi G., Ravasz E., Daugherty M.D., et al. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185 (2003) 5673-5684
9. Stribling D., and Perham R.N. Purification and characterization of two fructose diphosphate aldolases from Escherichia coli (Crookes' strain). Biochem. J. 131 (1973) 833-841
10. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 (2006) 2006.0008
11. Scamuffa M.D., and Caprioli R.M. Comparison of the mechanisms of two distinct aldolases from Escherichia coli grown on gluconeogenic substrates. Biochim. Biophys. Acta 614 (1980) 583-590
12. + symport at 91 min on the linkage map of Escherichia coli K12. J. Biol. Chem. 259 (1984) 1520-1525
13. Rosenkrands I., Slayden R.A., Crawford J., Aagaard C., Barry III C.E., and Andersen P. Hypoxic response of Mycobacterium tuberculosis studied by metabolic labeling and proteome analysis of cellular and extracellular proteins. J. Bacteriol. 184 (2002) 3485-3491
14. Bai N.J., Pai M.R., Murthy P.S., and Venkitasubramanian T.A. Effect of oxygen tension on the aldolases of Mycobacterium tuberculosis H37Rv. FEBS Lett. 45 (1974) 68-70
15. Rukseree, K. (2007). Fructose-1,6-biphosphate aldolase as a potential drug target for tuberculosis. Ph.D. dissertation, Mahidol University.
16. Zhang Y. The magic bullets and tuberculosis drug targets. Annu. Rev. Pharmacol. Toxicol. 45 (2005) 529-564
17. Fonvielle M., Weber P., Dabkowska K., and Therisod M. New highly selective inhibitors of class II fructose-1,6-bisphosphate aldolases. Bioorg. Med. Chem. Lett. 14 (2004) 2923-2926
18. Gavalda S., Braga R., Dax C., Vigroux A., and Blonski C. N-Sulfonyl hydroxamate derivatives as inhibitors of class II fructose-1,6-diphosphate aldolase. Bioorg. Med. Chem. Lett. 15 (2005) 5375-5377
19. Nakahara K., Yamamoto H., Miyake C., and Yokota A. Purification and characterization of class-I and class-II fructose-1,6-bisphosphate aldolases from the cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol. 44 (2003) 326-333
20. Plaumann M., Pelzer-Reith B., Martin W.F., and Schnarrenberger C. Multiple recruitment of class-I aldolase to chloroplasts and eubacterial origin of eukaryotic class-II aldolases revealed by cDNAs from Euglena gracilis. Curr. Genet. 31 (1997) 430-438
21. Sauve V., and Sygusch J. Molecular cloning, expression, purification, and characterization of fructose-1,6-bisphosphate aldolase from Thermus aquaticus. Protein Expression Purif. 21 (2001) 293-302
22. Cooper S.J., Leonard G.A., McSweeney S.M., Thompson A.W., Naismith J.H., Qamar S., et al. 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 (1996) 1303-1315
23. Janin J., Miller S., and Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204 (1988) 155-164
24. Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372 (2007) 774-797
25. Hall D.R., Leonard G.A., Reed C.D., Watt C.I., Berry A., and Hunter W.N. The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. J. Mol. Biol. 287 (1999) 383-394
26. Alberts I.L., Nadassy K., and Wodak S.J. Analysis of zinc binding sites in protein crystal structures. Protein Sci. 7 (1998) 1700-1716
27. Qamar S., Marsh K., and Berry A. 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 (1996) 154-161
28. Zgiby S.M., Thomson G.J., Qamar S., and Berry A. Exploring substrate binding and discrimination in fructose 1,6-bisphosphate and tagatose 1,6-bisphosphate aldolases. Eur. J. Biochem. 267 (2000) 1858-1868
29. May M., Mehboob S., Mulhearn D.C., Wang Z., Yu H., Thatcher G.R., et al. Structural and functional analysis of two glutamate racemase isozymes from Bacillus anthracis and implications for inhibitor design. J. Mol. Biol. 371 (2007) 1219-1237
30. Zgiby S., Plater A.R., Bates M.A., Thomson G.J., and Berry A. 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 (2002) 131-140
31. Thanki N., Zeelen J.P., Mathieu M., Jaenicke R., Abagyan R.A., Wierenga R.K., and Schliebs W. Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop. Protein Eng. 10 (1997) 159-167
32. Plater A.R., Zgiby S.M., Thomson G.J., Qamar S., Wharton C.W., and Berry A. Conserved residues in the mechanism of the E. coli class II FBP-aldolase. J. Mol. Biol. 285 (1999) 843-855
33. Dalby A., Dauter Z., and Littlechild J.A. Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications. Protein Sci. 8 (1999) 291-297
34. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: Carter Jr C.W., and Sweet R.M. (Eds). Methods in Enzymology. Macromolecular Crystallography, Part A 276 (1997), Academic Press, New York, NY
35. Bates P.A., Kelley L.A., MacCallum R.M., and Sternberg M.J. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins Suppl 5 (2001) 39-46
36. Collaborative Computational Project No. 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 (1994) 760-763
37. Painter J., and Merritt E.A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr., Sect. D: Biol. Crystallogr. 62 (2006) 439-450