Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase

EMBO Journal

Volumn 22, Issue 16, 2003, Pages 4038-4048

  Leys, David ^a   Basran, Jaswir ^a   Scrutton, Nigel S ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

'Active' formaldehyde; Arthrobacter globiformis; Channelling; Crystal structure; Dimethylglycine oxidase

Indexed keywords

BACTERIAL ENZYME; DIMETHYLGLYCINE; DIMETHYLGLYCINE OXIDASE; FORMALDEHYDE; METHYLENETETRAHYDROFOLIC ACID; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTHROBACTER; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; ENZYME BINDING; ENZYME METABOLISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ARTHROBACTER; BINDING SITES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; FLAVIN-ADENINE DINUCLEOTIDE; FORMALDEHYDE; HYDROGEN PEROXIDE; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; OXIDOREDUCTASES ACTING ON CH-NH GROUP DONORS; PROTEIN BINDING; SEQUENCE HOMOLOGY, AMINO ACID; TETRAHYDROFOLATES;

ACTINOBACTERIA (CLASS); ARTHROBACTER; ARTHROBACTER GLOBIFORMIS; BACTERIA (MICROORGANISMS); UNCULTURED ACTINOMYCETE;

EID: 0041465718     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg395     Document Type: Article

References (32)

1. Basran, J., Sutcliffe, M.J. and Scrutton, N.S. (2001) Optimising the Michaelis complex of trimethylamine dehydrogenase: identification of interactions that perturb the ionization of substrate and facilitate catalysis with trimethylamine base. J. Biol. Chem., 276, 42887-42892.
2. Basran, J., Bhanji, N., Basran, A., Nietlispach, D., Mistry, S., Meskys, R. and Scrutton, N.S. (2002) Mechanistic aspects of the covalent flavoprotein dimethylglycine oxidase of Arthrobacter globiformis studied by stopped-flow spectrophotometry. Biochemistry, 41, 4733-4743.
3. Binda, C., Coda, A., Angelini, R., Federico, R., Ascenzi, P. and Mattevi, A. (1999) A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase, Structure Fold. Des., 7, 265-276.
4. Binzak, B.A. et al. (2001) Cloning of dimethylglycine dehydrogenase and a new human inborn error of metabolism, dimethylglycine dehydrogenase deficiency. Am. J. Hum. Genet., 68, 839-847.
5. Boch, J., Kempf, B. and Bremer, E. (1994) Osmoregulation in Bacillus subtilis: synthesis of the osmoprotectant glycine betaine from exogenously provided choline. J. Bacteriol., 176, 5364-5371.
6. Cecchini, G., Schroder, I., Gunsalus, R.P. and Maklashina, E. (2002) Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta, 1553, 140-157.
7. CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D, 50, 760-763.
8. Cook, R.J., Misono, K.S. and Wagner, C. (1984) Identification of the covalently bound flavin of dimethylglycine dehydrogenase and sarcosine dehydrogenase from rat liver mitochondria. J. Biol. Chem., 259, 12475-12480.
9. Cordes, E.H. and Jencks, W.P. (1963) The mechanism of hydrolysis of Schiff bases derived from aliphatic amines. J. Am. Chem. Soc., 85, 2843-2848.
10. DeLano, W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
11. Eschenbrenner, M. and Jorns, M.S. (1999) Cloning and mapping of the cDNA for human sarcosine dehydrogenase, a flavoenzyme defective in patients with sarcosinemia. Genomics, 59, 300-308.
12. Eschenbrenner, M., Chlumsky, L.J., Khanna, P., Strasser, F. and Joms, M.S. (2001) Organization of the multiple coenzymes and subunits and role of the covalent flavin link in the complex heterotetrameric sarcosine oxidase. Biochemistry, 40, 5352-5367.
13. Fujiwara, K., Okamura-Ikeda, K. and Motokawa, Y. (1984) Mechanism of the glycine cleavage reaction. Further characterization of the intermediate attached to H-protein and of the reaction catalyzed by T-protein. J. BioL Chem., 259, 10664-10668.
14. Holm, L. and Sander, C. (1999) Protein folds and families: sequence and structure alignments. Nucleic Acids Res., 27, 244-247.
15. Huang, X., Holden, H.M. and Raushel, F.M. (2001) Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu. Rev. Biochem., 70, 149-180.
16. Jang, M.H., Basran, J., Scrutton, N.S. and Hille, R. (1999) The reaction of trimethylamine dehydrogenase with trimethylamine. J. Biol. Chem., 274, 13147-13154.
17. Kohls, D., Sulea, T., Purisima, E.O., MacKenzie, R.E. and Vrielink, A. (2000) The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase: implications for substrate channeling in a bifunctional enzyme. Structure Fold. Des., 8, 35-46.
18. Kvalnes-Krick, K. and Jorns, M.S. (1987) Interaction of tetrahydrofolate and other folate derivatives with bacterial sarcosine oxidase. Biochemistry, 26, 7391-7395.
19. Lawrence, M.C. and Colman, P.M. (1993) Shape complementarity at protein-protein interfaces. J. Mol. Biol., 234, 946-950.
20. Lawson, J.E., Park, S.H., Mattison, A.R., Yan, J. and Reed, L.J. (1997) Cloning, expression and properties of the regulatory subunit of bovine pyruvate dehydrogenase phosphatase. J. Biol. Chem., 272, 31625-31629.
21. Meskys, R., Harris, R.J., Casaite, V., Basran, J. and Scrutton, N.S. (2001) Organization of the genes involved in dimethylglycine and sarcosine degradation in Arthrobacter spp.: implications for glycine betaine catabolism. Eur. J. Biochem., 268, 3390-3398.
22. Miller, J.R. and Edmondson, D.E. (1999) Structure-activity relationships in the oxidation of para-substituted benzylamine analogues by recombinant human liver monoamine oxidase A. Biochemistry, 38, 13670-13683.
23. Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D, 53, 240-255.
24. Nicholls, A., Sharp, K.A. and Honig, B. (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281-296.
25. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
26. Perrakis, A., Morris, R. and Lamzin, V.S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol., 6, 458-463.
27. Porter, D.H., Cook, R.J. and Wagner, C. (1985) Enzymatic properties of dimethylglycine dehydrogenase and sarcosine dehydrogenase from rat liver. Arch. Biochem. Biophys., 243, 396-407.
28. Roussel, A. and Cambillau, C. (1996) TURBO-FRODO Manual. AFMB-CNRS, Marseille.
29. Schreuder, H.A., Mattevi, A., Obmolova, G., Kalk, K.H., Hol, W.G., van der Bolt, F.J. and van Berkel, W.J. (1994) Crystal structures of wild-type p-hydroxybenzoate hydroxylase complexed with 4-amino-benzoate,2,4-dihydroxybenzoate and 2-hydroxy-4-aminobenzoate and of the Tyr222Ala mutant complexed with 2-hydroxy-4-aminobenzoate. Evidence for a proton channel and a new binding mode of the flavin ring. Biochemistry, 33, 10161-10170.
30. Steenkamp, D.J. and Husain, M. (1982) The effect of tetrahydrofolate on the reduction of electron transfer flavoprotein by sarcosine and dimethylglycine dehydrogenases. Biochem. J., 203, 707-715.
31. Toone, J.R., Applegarth, D.A., Coulter-Mackie, M.B. and James, E.R. (2000) Biochemical and molecular investigations of patients with nonketotic hyperglycinemia. Mol. Genet. Metab., 70, 116-121.
32. Trickey, P., Wagner, M.A., Jorns, M.S. and Mathews, F.S. (1999) Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme. Structure Fold. Des., 7, 331-345.