Conformational changes in the catalytic cycle of protochlorophyllide oxidoreductase: What lessons can be learnt from dihydrofolate reductase?

Biochemical Society Transactions

Volumn 37, Issue 2, 2009, Pages 354-357

  Heyes, Derren J ^a   Scrutton, Nigel S ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Catalytic cycle; Chlorophyll biosynthesis; Conformational change; Dihydrofolate reductase (DHFR); Protein dynamics; Protochlorophytlide oxidoreductase

Indexed keywords

DIHYDROFOLATE REDUCTASE; OXIDOREDUCTASE; PROTOCHLOROPHYLLIDE OXIDOREDUCTASE; UNCLASSIFIED DRUG; PROTOCHLOROPHYLLIDE REDUCTASE;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME KINETICS; ENZYME MECHANISM; ENZYME RELEASE; ENZYME STRUCTURE; LIGAND BINDING; MOTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN STRUCTURE; CHEMISTRY; KINETICS; METABOLISM; PHOTOCHEMISTRY; PROTEIN CONFORMATION; REVIEW;

CATALYSIS; CATALYTIC DOMAIN; KINETICS; OXIDOREDUCTASES ACTING ON CH-CH GROUP DONORS; PHOTOCHEMISTRY; PROTEIN CONFORMATION;

EID: 65549145871     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0370354     Document Type: Article

References (28)

1. Heyes, D.J. and Hunter, C.N. (2005) Making light work of enzyme catalysis: protochlorophyllide oxidoreductase. Trends Biochem. Sci. 30, 642-649
2. Lebedev, N. and Timko, M.P. (1998) Protochlorophyllide photoreduction. Photosyn. Res. 58, 5-23
3. Aronsson, H., Sundqvist, C. and Dahlin, C. (2003) POR hits the road: import and assembly of a plastid protein. Plant Mol. Biol. 51, 1-7
4. Wilks, H.M. and Timko, M.P. (1995) A light-dependent complementation system for analysis of NADPH:protochlorophyllide oxidoreductase: identification and mutagenesis of two conserved residues that are essential for enzyme activity. Proc. Natl. Acad. Sci. U.S.A. 92, 724-728
5. Lebedev, N. and Timko, M.P. (1999) Protochlorophyllide oxidoreductase B-catalyzed protochlorophyllide photoreduction in vitro: insight into the mechanism of chlorophyll formation in light-adapted plants. Proc. Natl. Acad. Sci. U.S.A. 96, 9954-9959
6. 279 stabilize NADPH within the catalytic site of NADPH:protochlorophyllide oxidoreductase and are involved in the formation of the enzyme photoactive state. Biochemistry 40, 12562-12574
7. Heyes, D.J., Ruban, A.V., Wilks, H.M. and Hunter, C.N. (2002) Enzymology below 200 K: the kinetics and thermodynamics of the photochemistry catalyzed by protochlorophyllide oxidoreductase. Proc. Natl. Acad. Sci. U.S.A. 99, 11145-11150
8. Heyes, D.J., Ruban, A.V. and Hunter, C.N. (2003) Protochlorophyllide oxidoreductase: 'dDark' reactions of a light-driven enzyme. Biochemistry 42, 523-528
9. Heyes, D.J. and Hunter, C.N. (2004) Identification and characterization of the product release steps within the catalytic cycle of protochlorophyllide oxidoreductase. Biochemistry 43, 8265-8271
10. Heyes, D.J., Heathcote, P., Rigby, S.E.J., Palacios, M.A., van Grondelle, R. and Hunter, C.N. (2006) The first catalytic step of the light-driven enzyme protochlorophyllide oxidoreductase proceeds via a charge transfer complex. J. Biol. Chem. 281, 26847-26853
11. Heyes, D.J., Sakuma, M. and Scrutton, N.S. (2007) Laser excitation studies of the product release steps in the catalytic cycle of the light-driven enzyme, protochlorophyllide oxidoreductase. J. Biol. Chem. 282, 32015-32020
12. Heyes, D.J., Menon, B.R.K., Sakuma, M. and Scrutton, N.S. (2008) Conformational events during ternary enzyme-substrate complex formation are rate limiting in the catalytic cycle of the light-driven enzyme protochlorophyllide oxidoreductase. Biochemistry 47, 10991-10998
13. Jörnvall, H., Persson, B., Krook, M., Atrian, S., Gonzalez-Duarte, R., Jeffery, J. and Ghosh, D. (1995) Short-chain dehydrogenases/ reductases (SDR). Biochemistry 34, 6003-6013
14. Oppermann, U., Filling, C., Hult, M., Shafqat, N., Wu, X., Lindh, M., Shafqat, J., Nordling, E., Kallberg, Y., Persson, B. and Jörnvall, H. (2003) Short-chain dehydrogenases/reductases (SDR): the 2002 update. Chem. Biol. Interact. 143-144, 247-253
15. Kohen, A., Cannio, R., Bartolucci, S. and Klinman, J.P. (1999) Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase. Nature 399, 496-499
16. Boehr, D.D., McElheny, D., Dyson, H.J. and Wright, P.E. (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 1638-1642
17. Townley, H.E., Sessions, R.B., Clarke, A.R., Dafforn, T.R. and Griffiths, W.T. (2001) Protochlorophyllide oxidoreductase: a homology model examined by site-directed mutagenesis. Proteins 44, 329-335
18. Schnell, J.R., Dyson, H.J. and Wright, P.E. (2004) Structure, dynamics and catalytic function of dihydrofolate reductase. Annu. Rev. Biophys. Biomol. Struct. 33, 119-140
19. Fierke, C.A., Johnson, K.A. and Benkovic, S.J. (1987) Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry 26, 4085-4092
20. Matthews, D.A., Alden, R.A., Bolin, J.T., Freer, S.T., Hamlin, R., Xuong, N., Kraut, J., Poe, M., Williams, M. and Hoogsteen, K. (1977) Dihydrofolate reductase: X-ray structure of the binary complex with methotrexate. Science 197, 452-455
21. Sawaya, M.R. and Kraut, J. (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 36, 586-603
22. Osborne, M.J., Schnell, J., Benkovic, S.J., Dyson, H.J. and Wright, P.E. (2001) Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry 40, 9846-9859
23. Venkitakrishnan, R.P., Zaborowski, E., McElheny, D., Benkovic, S.J., Dyson, H.J. and Wright, P.E. (2004) Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle. Biochemistry 43, 16046-16055
24. Cameron, C.E. and Benkovic, S.J. (1997) Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry 36, 15792-15800
25. Miller, G.P. and Benkovic, S.J. (1998) Strength of an interloop hydrogen bond determines the kinetic pathway in catalysis by Escherichia coli dihydrofolate reductase. Biochemistry 37, 6336-6342
26. Miller, G.P. and Benkovic, S.J. (1998) Deletion of a highly motional residue affects formation of the Michaelis complex for Escherichia coli dihydrofolate reductase. Biochemistry 37, 6327-6335
27. Miller, G.P., Wahnon, D.C. and Benkovic, S.J. (2001) Interloop contacts modulate ligand cycling during catalysis by Escherichia coli dihydrofolate reductase. Biochemistry 40, 867-875
28. Rajagopalan, P.T., Lutz, S. and Benkovic, S.J. (2002) Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates. Biochemistry 41, 12618-12628