On the catalytic role of the active site residue E121 of E. coli l-aspartate oxidase

Biochimie

Volumn 92, Issue 10, 2010, Pages 1335-1342

  Tedeschi, Gabriella ^a   Nonnis, Simona ^a   Strumbo, Bice ^a   Cruciani, Gabriele ^b   Carosati, Emanuele ^b   Negri, Armando ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF PERUGIA   (Italy)

Author keywords

Flavoprotein oxidase; Fumarate reductase; L aspartate oxidase; NadB; Succinate dehydrogenase

Indexed keywords

ASPARTATE OXIDASE; DEXTRO ASPARTIC ACID; FUMARATE REDUCTASE; GLUTAMIC ACID; MUTANT PROTEIN;

ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ESCHERICHIA COLI; MOLECULAR DOCKING; NONHUMAN; PROTEIN BINDING;

AMINO ACID OXIDOREDUCTASES; CATALYSIS; CATALYTIC DOMAIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GLUTAMIC ACID; MUTATION, MISSENSE; PROTEIN BINDING; SUBSTRATE SPECIFICITY; SUCCINATE DEHYDROGENASE;

EID: 77957163782     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2010.06.015     Document Type: Article

References (36)

1. Gerdes S.Y., Scholle M.D., D'Souza M., Bernal A., Baev M.V., Farrell M., Kurnasov O.V., Daugherty M.D., Mseeh F., Polanuyer B.M., Campbell J.W., Anantha S., Shatalin K.Y., Chowdhury S.A.K., Fonstein M.Y., Osterman A.L. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J. Bacteriol. 2002, 184:4555-4572.
2. Mortarino M., Negri A., Tedeschi G., Simonic T., Duga S., Gassen H.S., Ronchi S. l-aspartate oxidase from Escherichia coli. I. Characterization of coenzyme binding and product inhibition. Eur. J. Biochem. 1996, 239:418-426.
3. Tedeschi G., Negri A., Mortarino M., Ceciliani F., Simonic T., Faotto L., Ronchi S. l-aspartate oxidase from Escherichia coli. II. Interaction with C4-dicarboxylic acids and identification of a novel l-aspartate:fumarate oxidoreductase activity. Eur. J. Biochem. 1996, 239:427-433.
4. Tedeschi G., Zetta L., Negri A., Mortarino M., Ceciliani F., Ronchi S. Redox potentials and quinone reductase activity of l-aspartate oxidase from E. coli. Biochemistry 1997, 36:16221-16230.
5. Mattevi A., Tedeschi G., Bacchella L., Coda A., Negri A., Ronchi S. Structure of l-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family. Structure 1999, 7:745-756.
6. Bossi R.T., Negri A., Tedeschi G., Mattevi A. Structure of FAD-bound l-aspartate oxidase: insight into substrate specificity and catalysis. Biochemistry 2002, 41:3018-3024.
7. Iverson T.M., Luna-Chavez C., Cecchini G., Rees D.C. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 1999, 284:1961-1966.
8. Lancaster C.R.D., Kroger A., Auer M., Michel H. Structure of fumarate reductase from Wolinwlla succinogenes at 2.2 Å resolution. Nature 1999, 402:377-385.
9. Taylor P., Pealing S.L., Reid G.A., Chapman K.S., Walkinshaw D.W. Structural and mechanistic mapping of a unique fumarate reductase. Nat. Struct. Biol. 1999, 6:1108-1112.
10. Leys D., Tsapin A.S., Nealson K.H., Meyer T.E., Cusanovich M.A., Van Beeumen J.J. Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1. Nat. Struct. Biol. 1999, 6:1113-1117.
11. Bamford V., Dobbin P.S., Richardson D.J., Hemmings A.M. Open conformation of a flavocytochrome c3 fumarate reductase. Nat. Struct. Biol. 1999, 6:1104-1107.
12. Lancaster C.R., Gross R., Simon J. A third crystal form of Wolinella succinogenes quinol:fumarate reductase reveals domain closure at the site of fumarate reduction. Eur. J. Biochem. 2001, 268:1820-1827.
13. Yankovskaya V., Horsefield R., Törnroth S., Luna-Chavez C., Miyoshi H., Léger C., Byrne B., Cecchini G., Iwata S. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 2003, 299:700-704.
14. Sun F., Huo X., Zhai Y., Wang A., Xu J., Su D., Bartlam M., Rao Z. Crystal structure of mitochondrial respiratory membrane protein complex II. Cell 2005, 121:1043-1057.
15. Huang L.S., Sun G., Cobessi D., Wang A.C., Shen J.T., Tung E.Y., Anderson V.E., Berry E.A. 3-Nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. J. Biol. Chem. 2006, 281:5965-5972.
16. Fritz G., Roth A., Schiffer A., Buchert Thomas, Bourenkov G., Bartunik H.D., Huber H., Stetter K.O., Kroneck P.M.H., Ermler U. Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution. Proc. Natl. Acad. Sci. USA 2002, 99:1836-1841.
17. Sakuraba H., Yoneda K., Asai I., Tsuge H., Katunuma N., Ohshima T. Structure of l-aspartate oxidase from the hyperthermophilic archaeon Sulfolobus tokodaii. Biochim. Biophys. Acta 2008, 1784:563-571.
18. Lancaster C.R.D. Succinate: quinone oxidoreductases. Handbook of Metalloproteins 2001, 379-401. Wiley, Hoboken. A. Messerschmidt, R. Huber, K. Wieghardt, T. Poulos (Eds.).
19. Tedeschi G., Negri A., Ceciliani F., Mattevi A., Ronchi S. Structural characterization of l-aspartate oxidase and identification of an interdomain loop by limited proteolysis. Eur. J. Biochem. 1999, 260:896-903.
20. Doherty M.K., Pealing S.L., Miles C.S., Moysey R., Taylor P., Walkinshaw M.D., Reid G.A., Chapman S.K. Identification of the active site acid/base catalyst in a bacterial fumarate reductase: a kinetic and crystallographic study. Biochemistry 2000, 39:10695-10701.
21. Mowat C.G., Moysey R., Miles C.S., Leys D., Doherty M.K., Taylor P., Walkinshaw M.D., Reid G.A., Chapman S.K. Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase. Biochemistry 2001, 40:12292-12298.
22. Tedeschi G., Ronchi S., Simonic T., Treu C., Mattevi A., Negri A. Probing the active site of l-aspartate oxidase by site-directed mutagenesis: role of basic residues in fumarate reduction. Biochemistry 2001, 40:4738-4744.
23. Pankhurst K.L., Mowat C.G., Rothery E.L., Hudson J.M., Jones A.K., Miles C.S., Walkinshaw M.D., Armstrong F.A., Reid G.A., Chapman S.K. A proton delivery pathway in the soluble fumarate reductase from Shewanella frigidimarina. J. Biol. Chem. 2006, 281:20589-20597.
24. Tomasiak T.M., Maklashina E., Cecchini G., Iverson T.M. A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II. J. Biol. Chem. 2008, 283:15460-15468.
25. http://www.moldiscovery.com.
26. Goodford P.J. A computational procedure for determining energetically favourable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28:849-857.
27. Carosati E., Sciabola S., Cruciani G. Hydrogen bonding interactions of covalently bonded fluorine atoms: from crystallographic data to a new angular function in the GRID force field. J. Med. Chem. 2004, 47:5114-5125.
28. Negri A., Massey V., Williams C.H. d-Aspartate oxidase from beef kidney. J. Biol. Chem. 1987, 262:10026-10034.
29. Wardrope C., Mowat C.G., Walkinshaw M.D., Reid G.A., Chapman S.K. Fumarate reductase: structural and mechanistic insights from the catalytic reduction of 2-methylfumarate. FEBS Lett. 2006, 580:1677-1680.
30. Guillén Schlippe Y.V., Hedstrom L. A twisted base? The role of arginine in enzyme-catalyzed proton abstractions. Arch. Biochem. Biophys. 2005, 433:266-278.
31. Walsh C. Enzymatic reaction mechanisms 1979, W.H. Freeman and Company, New York, 382-388.
32. Panchenko M.V., Vinogradov A.D. Direct demonstration of enol-oxaloacetate as an immediate product of malate oxidation by the mammalian succinate dehydrogenase. FEBS Lett. 1991, 286:76-78.
33. Fell L.M., Francis J.T., Holmes J.L., Terlouw J.K. The intriguing behaviour of (ionized) oxalacetic acid investigated by tandem mass spectrometry. Int. J. Mass Spectrom. Ion. Process. 1997, 165/166:179-194.
34. Maklashina E., Iverson T.M., Sher Y., Kotlyar V., Andréll J., Mirza O., Hudso J.M., Armstrong F.A., Rothery R.A., Weiner J.H., Cecchini G. Fumarate reductase and succinate oxidase activity of Escherichia coli complex II homologs are perturbed differently by mutation of the flavin binding domain. J. Biol. Chem. 2006, 281:11357-11365.
35. Huang L.S., Shen J.T., Wang A.C., Berry E.A. Crystallographic studies of the binding of ligands to the dicarboxylate site of complex II, and the identity of the ligand in the " oxaloacetate-inhibited" state. Biochim. Biophys. Acta 2006, 1757:1073-1083.
36. Reid G.A., Miles C.S., Moysey R.K., Pankhurst K.L., Chapman S.K. Catalysis in fumarate reductase. Biochim. Biophys. Acta 2000, 1459:310-315.