Cofactor-induced conformational rearrangements establish a catalytically competent active site and a proton relay conduit in FabG

Structure

Volumn 12, Issue 3, 2004, Pages 417-428

  Price, Allen C ^a   Zhang, Yong Mei ^a   Rock, Charles O ^a,b   White, Stephen W ^a,b  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3 OXOACYL ACYL CARRIER PROTEIN REDUCTASE; HYDROGEN; HYDROXYL GROUP; LYSINE; MUTANT PROTEIN; NICOTINAMIDE; OXIDOREDUCTASE; PROTON; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; RIBOSE; SERINE; TYROSINE; UNCLASSIFIED DRUG; WATER;

ARTICLE; BINDING AFFINITY; BIOCHEMISTRY; CATALYSIS; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME DEFECT; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; HYDROGEN BOND; MOLECULE; PRIORITY JOURNAL; PROTON TRANSPORT;

ALCOHOL OXIDOREDUCTASES; BINDING SITES; CALCIUM; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; NADP; PROTEIN BINDING; PROTEIN CONFORMATION; PROTONS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 1542602992     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.02.008     Document Type: Article

References (35)

1. Alberts A.W., Majerus P.W., Talamo B., Vagelos P.R. Acyl carrier protein II. Intermediary reactions of fatty acid synthesis. Biochemistry. 3:1964;1563-1571.
2. 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.et al. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
3. Campbell J.W., Cronan J.E. Jr. Bacterial fatty acid biosynthesis. targets for antibacterial drug discovery Annu. Rev. Microbiol. 55:2001;305-332.
4. 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. 320:2002;249-261.
5. Cronan J.E. Jr., Rock C.O. Biosynthesis of membrane lipids In Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology, J. L graham and F.C. Neidhardt. 1996;612-636 American Society for Microbiology, Washington, D.C..
6. Davies C., Heath R.J., White S.W., Rock C.O. The 1.8 Å cystal structure and active site architecture of β-ketoacyl-[acyl carrier protein] synthase III (FabH) from Escherichia coli. Structure. 8:2000;185-195.
7. Fawcett T., Copse C.L., Simon J.W., Slabas A.R. Kinetic mechanism of NADH-enoyl-ACP reductase from Brassica napus. FEBS Lett. 484:2000;65-68.
8. Filling C., Berndt K.D., Benach J., Knapp S., Prozorovski T., Nordling E., Ladenstein R., Jörnvall H., Oppermann U. Critical residues for structure and catalysis in short-chain dehydrogenases/reductases. J. Biol. Chem. 277:2002;25677-25684.
9. Fisher M., Kroon J.T., Martindale W., Stuitje A.R., Slabas A.R., Rafferty J.B. The X-ray structure of Brassica napus β-ketoacyl carrier protein reductase and its implications for substrate binding and catalysis. Structure. 8:2000;339-347.
10. Ghosh D., Pletnev V.Z., Zhu D.W., Wawrzak Z., Duax W.L., Pangborn W., Labrie F., Lin S.X. Structure of human estrogenic 17β-hydroxysteroid dehydrogenase at 2.20 Å resolution. Structure. 3:1995;503-513.
11. Grimm C., Maser E., Mobus E., Klebe G., Reuter K., Ficner R. The crystal structure of 3α-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family. J. Biol. Chem. 275:2000;41333-41339.
12. Heath R.J., White S.W., Rock C.O. Lipid biosynthesis as a target for antibacterial agents. Prog. Lipid Res. 40:2001;467-497.
13. Jackowski S., Rock C.O. Forty years of fatty acid biosynthesis. Biochem. Biophys. Res. Commun. 292:2002;1155-1166.
14. Jörnvall H., Persson B., Krook M., Atrian S., Gonzalez-Duarte R., Jeffery J., Ghosh D. Short-chain dehydrogenases/reductases (SDR). Biochemistry. 34:1995;6003-6013.
15. Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950.
16. Laskowski R.A., McArthur M.W., Moss D.S., Thornton J.M. Procheck. a program to check the quality of protein structures J. Appl. Crystallogr. 26:1993;282-291.
17. Merritt E.A., Murphy M.E.P. Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D50:1994;869-873.
18. Meyer E. Internal water molecules and H-bonding in biological macromolecules. a review of structural features with functional implications Protein Sci. 1:1992;1543-1562.
19. Navaza J. AMoRe - an automated package for molecular replacement. Acta Crystallogr. A50:1994;869-873.
20. Oppermann U., Filling C., Hult M., Shafqat N., Wu X., Lindh M., Shafqat J., Nordling E., Kallberg Y., Persson B.et al. Short-chain dehydrogenases/ reductases (SDR). the 2002 update Chem. Biol. Interact. 143-144:2003;247-253.
21. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
22. + conduction in the single-file water chain of the gramicidin channel. Biophys. J. 82:2002;2304-2316.
23. Price A.C., Zhang Y.-M., Rock C.O., White S.W. The structure of β-ketoacyl-[acyl carrier protein] reductase from Escherichia coli. negative cooperativity and its structural basis Biochemistry. 40:2001;12772-12781.
24. Price A.C., Rock C.O., White S.W. The 1.3 Å resolution crystal structure of β-ketoacyl-acyl carrier protein synthase II from Streptococcus pneumoniae. J. Bacteriol. 185:2003;4136-4143.
25. Qiu X., Janson C.A., Smith W.W., Head M., Lonsdale J., Konstantinidis A.K. Refined structures of β-ketoacyl-acyl carrier protein synthase III. J. Mol. Biol. 307:2001;341-356.
26. Sheldon P.S., Kekwick R.G., Smith C.G., Sidebottom C., Slabas A.R. 3-Oxoacyl-[ACP] reductase from oilseed rape (Brassica napus). Biochim. Biophys. Acta. 1120:1992;151-159.
27. Smith S., Witkowski A., Joshi A.K. Structural and functional organization of the animal fatty acid synthase. Prog. Lipid Res. 42:2003;289-317.
28. Somoza J.R., Menon S., Schmidt H., Joseph-McCarthy D., Dessen A., Stahl M.L., Somers W.S., Sullivan F.X. Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose. Structure. 8:2000;123-135.
29. Tanabe T., Tanaka N., Uchikawa K., Kabashima T., Ito K., Nonaka T., Mitsui Y., Tsuru M., Yoshimoto T. Roles of the Ser146, Tyr159, and Lys163 residues in the catalytic action of 7α-hydroxysteroid dehydrogenase from Escherichia coli. J. Biochem. (Tokyo). 124:1998;634-641.
30. Tanaka N., Nonaka T., Tanabe T., Yoshimoto T., Tsuru D., Mitsui Y. Crystal structures of the binary and ternary complexes of 7α- hydroxysteroid dehydrogenase from Escherichia coli. Biochemistry. 35:1996;7715-7730.
31. Toomey R.E., Wakil S.J. Studies on the mechanism of fatty acid synthesis. XV. Preparation and general properties of β-ketoacyl acyl carrier protein reductase from Escherichia coli. Biochim. Biophys. Acta. 116:1966;189-197.
32. Zhang Y., Cronan J.E. Jr. Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster. J. Bacteriol. 180:1998;3295-3303.
33. Zhang Y.-M., Rao M.S., Heath R.J., Price A.C., Olson A.J., Rock C.O., White S.W. Identification and analysis of the acyl carrier protein (ACP) docking site on β-ketoacyl-ACP synthase III. J. Biol. Chem. 276:2001;8231-8238.
34. Zhang Y.-M., Marrakchi H., White S.W., Rock C.O. The application of computational methods to explore the diversity and structure of bacterial fatty acid synthase. J. Lipid Res. 44:2003;1-10. a.
35. Zhang Y.-M., Wu B., Zheng J., Rock C.O. Key residues responsible for acyl carrier protein (ACP) and β-ketoacyl carrier protein reductase (FabG) interaction. J. Biol. Chem. in press:2003;. b.