Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA

Journal of Biochemistry

Volumn 134, Issue 2, 2003, Pages 297-304

  Satoh, Atsuko ^a   Nakajima, Yoshitaka ^a   Miyahara, Ikuko ^a   Hirotsu, Ken ^a   Tanaka, Takeyuki ^b   Nishina, Yasuzo ^c   Shiga, Kiyoshi ^c   Tamaoki, Haruhiko ^c   Setoyama, Chiaki ^c   Miura, Retsu ^c  

^a Osaka Prefecture University   (Japan)

^b KOBE UNIVERSITY   (Japan)

^c KUMAMOTO UNIVERSITY   (Japan)

Author keywords

Charge transfer complex; Flavoenzyme; Medium chain acyl CoA dehydrogenase; Molecular orbital calculation; Three dimensional structure; X ray crystallography

Indexed keywords

3 THIABUTANOIC ACID; 3 THIAOCTANOYL COENZYME A; BUTYRIC ACID DERIVATIVE; LUMIFLAVINE; MEDIUM CHAIN ACYL COENZYME A DEHYDROGENASE; OCTANOIC ACID DERIVATIVE; QUERCETIN; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CRYSTALLIZATION; CRYSTALLOGRAPHY; ELIMINATION REACTION; ENZYME ACTIVE SITE; ENZYME LOCALIZATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; MOLECULAR DYNAMICS; PHASE TRANSITION; PROTON TRANSPORT; REACTION ANALYSIS; STRUCTURE ANALYSIS; TRANSPORT KINETICS; X RAY CRYSTALLOGRAPHY;

ACYL COENZYME A; ACYL-COA DEHYDROGENASE; ANIMALS; ARGININE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ELECTROSTATICS; FLAVINS; GLUTAMIC ACID; KIDNEY; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; SPECTROPHOTOMETRY; SWINE;

EID: 12444298922     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvg143     Document Type: Article

References (24)

1. Crane, F.L., Mii, S., Hauge, J.G., Green, D.E., and Beinert, H. (1956) On the mechanism of dehydrogenase of fatty acyl derivatives of coenzyme A. I. The general fatty acyl coenzyme A dehydrogenase. J. Biol. Chem. 218, 701-716
2. Engel, P.C. (1992) Acyl-CoA dehydrogenases in Chemistry and Biochemistry of Flavoenzymes. (Müller, F., ed.) Vol. III, pp. 597-655, CRC Press, Boca Raton, Ann Arbor, London
3. Kim, J.J.-P, Wang, M., and Paschke, R. (1993) Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Proc. Natl Acad. Sci. USA 15, 7523-7527
4. Ghisla, S., Thorpe, C., and Massey, V. (1984) Mechanistic studies with general acyl-CoA dehydrogenase and butyryl-CoA dehydrogenase: Evidence for the transfer of β-hydrogen to the flavin N(5)-position as hydride. Biochemistry 23, 3154-3161
5. Lau, S.M., Brantley, R.K., and Thorpe, C. (1988) The reductive half-reaction in Acyl-CoA dehydrogenase from pig kidney: studies with thiaoctanoyl-CoA and oxaoctanoyl-CoA analogues. Biochemistry 27, 5089-5095
6. Tamaoki, H., Nishina, Y., Shiga, K, and Miura, R. (1999) Mechanism for the recognition and activation of substrate in medium-chain acyl-CoA dehydrogenase. J. Biochem. 125, 285-296
7. Gorelick, R.J., Mizzer, J.P., and Thorpe, C. (1982) Purification and properties of electron-transferring flavoprotein from pig kidney. Biochemistry 21, 6936-6942
8. Lau, S.-M., Powell, P., Buettner, H., Ghisla, S., and Thorpe, C. (1986) Medium-chain acyl coenzyme A dehydrogenase from pig kidney has intrinsic enoyl coenzyme A hydratase activity. Biochemistry 25, 4184-4189
9. Jancarik, J. and Kim, S.-H. (1991) Sparse matrix sampling: a screening method for crystallization of proteins, J. Appl. Crystallogr. 24, 409-411
10. Matthews, B.W. (1968) Solvent content of protein crystals. J. Mol. Biol. 33, 491-497
11. Otwinowski, Z. (1993) Data collection and processing in Proceedings of the CCP4 Study Weekend, pp.56-62, SERC Daresbury Laboratory, Warrington
12. Navaza, J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr A50, 157-163
13. Kim, J.-J.P. and Wu, J. (1988) Structure of the medium-chain acyl-CoA dehydrogenase from pig liver mitochondria at 3-Å resolution. Proc. Natl Acad. Sci. USA 85, 6677-6681
14. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.N., 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. D54, 905-921
15. Jones, T.A., Zou, J.-Y., Cowan, S.W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location errors in these models. Acta Crystallogr. A47, 110-119
16. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
17. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950
18. Esnouf, R.M. (1997) An extensively modified version of Molscript that includes greatly enhanced coloring capabilities. J. Mol. Graphics. 15, 132-134
19. Merritt, E.A. and Murphy, M.E.P. (1994) Raster3D version 2.0: a program for photorealistic molecular graphics. Acta Crystallogr. D50, 869-873
20. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Zakrzewski, V.G., Montgomery, Jr., J.A., Stratmann, R.E., Burant, J.C., Dapprich, S., Millam, J.M., Daniels, A.D., Kudin, K.N., Strain, M.C., Farkas, O., Tomasi, Barone, J.V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G.A., Ayala, P.Y., Cui, Q., Morokuma, K., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Cioslowski, J., V. Ortiz, J., Stefanov, B.B., Liu, G., Liashenko, Piskorz, A.P., Komaromi, I., Gomperts, R., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Andres, J.L., Gonzalez, C., Head-Gordon, M., Replogle, E.S., and Pople, J.A. (1998) Gaussian 98, Revision A.7 Gaussian, Pittsburgh PA
21. Becke, A.D. (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652
22. Lee, C., Yang, W., and Parr, R.G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B37, 785-789
23. Mulliken, R.S. (1955) Electronic population analysis on LCAO-MO molecular wave functions. I. J. Chem. Phys. 23, 1833-1840
24. Foresman, J.B. and Frisch, AE. (1996) Exploring Chemistry with Electronic Structure Methods, 2nd ed., pp. 194-197, Gaussian, Pittsburgh, PA