Crystal structure of FabG4 from Mycobacterium tuberculosis reveals the importance of C-terminal residues in ketoreductase activity

Journal of Structural Biology

Volumn 174, Issue 1, 2011, Pages 147-155

  Dutta, Debajyoti ^a   Bhattacharyya, Sudipta ^a   Mukherjee, Somnath ^a   Saha, Baisakhee ^a   Das, Amit Kumar ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY   (India)

Author keywords

Catalytic triad; Flavodoxin type fold; High molecular weight FabG; Mycobacterium tuberculosis; Short chain dehydrogenase reductase

Indexed keywords

3 HYDROXYACYL COENZYME A DEHYDROGENASE; LYSINE; OXIDOREDUCTASE; PROTEIN FABG4; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; SERINE; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR INTERACTION; MYCOBACTERIUM TUBERCULOSIS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PURIFICATION; REDUCTION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURE-ACTIVITY RELATIONSHIP;

MYCOBACTERIUM TUBERCULOSIS;

EID: 79952440532     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.11.012     Document Type: Article

References (34)

1. Banerjee A., Sugantino M., Sacchettini J.C., Jacobs W.R. The mabA gene from the inhA operon of Mycobacterium tuberculosis encodes a 3-ketoacyl reductase that fails to confer isoniazid resistance. Microbiology 1998, 144:2697-2704.
2. Bloch K. Fatty acid synthases from Mycobacterium phlei. Methods Enzymol. 1975, 35:84-90.
3. Bloch K. Control mechanisms for fatty acid synthesis in Mycobacterium smegmatis. Adv. Enzymol. Relat. Areas Mol. Biol. 1977, 45:1-84.
4. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72:248-254.
5. Boshoff H.I., Myers T.G., Copp B.R., McNeil M.R., Wilson M.A., Barry C.E. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004, 279:40174-40184.
6. CCP4, 1994. Collaborative computational project number 4. Acta Crystallogr., D 50, 760-763.
7. Cohen-Gonsaud M., Ducasse S., Hoh F., Zerbib D., Labesse G., Quemard A. Crystal structure of MabA from Mycobacterium tuberculosis, a reductase involved in long-chain fatty acid biosynthesis. J. Mol. Biol. 2002, 320:249-261.
8. Cohen-Gonsaud M., Ducasse-Cabanot S., Quemard A., Labesse G. Ligand-induced fit in mycobacterial MabA: the sequence-specific C-terminus locks the conformational change. Proteins 2005, 60:392-400.
9. Cole S.T., Brosch R., Parkhill J., Garnier T., et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393:537-544.
10. Cole S.T., Eiglmeier K., Parkhill J., James K.D., et al. Massive gene decay in the leprosy bacillus. Nature 2001, 409:1007-1011.
11. Durfee T., Nelson R., Baldwin S., Plunkett G., Burland V., Mau B., Petrosino J.F., Qin X., Muzny D.M., Ayele M., Gibbs R.A., Csörgo B., Pósfai G., Weinstock G.M., Blattner F.R. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 2008, 190:2597-2606.
12. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr., D 2004, 60:2126-2132.
13. Evans, P.R., 1993. In: Sawyer, L., Isaacs, N., Bailey, S. (Eds.), Proceedings of the CCP4 Study Weekend. Data Collection and Processing, Warrington, Daresbury Laboratory, pp. 114-122.
14. Fisher M., Kroon J.T., Martindale W., Stuitje A.R., Slabas A.R., Rafferty J.B. The X-ray structure of Brassica napus beta-keto acyl carrier protein reductase and its implications for substrate binding and catalysis. Structure 2000, 8:339-347.
15. Garnier J., Gibrat J.F., Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 1996, 266:540-553.
16. Gouet P., Courcelle E., Stuaet D.I., Metoz F. Espript: multiple sequence alignments in PostScript. Bioinformatics 1999, 15:305-308.
17. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 1993, 26:795-800.
18. Kikuchi S., Kusaka T. New malonyl-CoA-dependent fatty acid elongati on system in Mycobacterium smegmatis. J. Biochem. (Tokyo) 1982, 92:839-844.
19. Kinsella R.J., Fitzpatrick D.A., Creevey C.J., McInerney J.O. Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication. Proc. Natl. Acad. Sci. USA 2003, 100:10320-10325.
20. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
21. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
22. Marrakchi H., Ducasse S., Labesse G., Margeat E., Montrozier H., Emorine L., Charpentier X., Lanéelle G., Quémard A. Biochemical and structural studies of the Mycobacterium tuberculosis MabA (FabG1) protein involved in the fatty acid elongation system, FAS-II. Microbiology 2002, 148:951-960.
23. Marri P.R., Bannantine J.P., Golding G.B. Comparative genomics of metabolic pathways in Mycobacterium species: gene duplication, gene decay and lateral gene transfer. FEMS Microbiol. Rev. 2006, 30:906-925.
24. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J. Appl. Crystallogr. 2007, 40:658-674.
25. Miller D.J., Zhang Y.M., Rock C.O., White S.W. Structure of RhlG, an essential beta-ketoacyl reductase in the rhamnolipid biosynthetic pathway of Pseudomonas aeruginosa. J. Biol. Chem. 2006, 281:18025-18032.
26. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr., D 1997, 53:240-255.
27. Page R.D.M. TreeView: an application to display phylogenetic trees on personal computers. Bioinformatics 1996, 12:357-358.
28. Poncet-Montange G., Ducasse-Cabanot S., Quemard A., Labesse G., Cohen-Gonsaud M. Lack of dynamics in the MabA active site kills the enzyme activity: practical consequences for drug-design studies. Acta Crystallogr., D 2007, 63:923-925.
29. Price A.C., Zhang Y.M., Rock C.O., White S.W. Cofactor-induced conformational rearrangements establish a catalytically competent active site and a proton relay conduit in FabG. Structure 2004, 12:417-428.
30. Sacco E., Slama N., Bäckbro K., Parish T., Laval F., Daffé M., Eynard N., Quémard A. Revisiting the assignment of Rv0241c to fatty acid synthase type II of Mycobacterium tuberculosis. J. Bacteriol. 2010, 192:4037-4044.
31. Takayama K., Wang C., Besra G.S. Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. Clin. Microb. Rev. 2005, 18:81-101.
32. Wickramasinghe S.R., Inglis K.A., Urch J.E., Muller S., van Aalten D.M.F., Fairlamb A.H. Kinetic, inhibition and structural studies on 3-oxoacyl-ACP reductase from Plasmodium falciparum, a key enzyme in fatty acid biosynthesis. Biochem. J. 2006, 393:447-457.
33. Yang J.K., Park M.S., Waldo G.S., Suh S.W. Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 2003, 100:455-460.
34. Zaccai N.R., Carter L.G., Berrow N.S., Sainsbury S., Nettleship J.E., Walter T.S., Harlos K., Owens R.J., Wilson K.S., Stuart D.I., Esnouf R.M. Crystal structure of a 3-oxoacyl-(acylcarrier protein) reductase (BA3989) from Bacillus anthracis at 2.4-A resolution. Proteins 2008, 70:562-567.