Kinetic and mechanistic analysis of the Escherichia coli ribD-encoded bifunctional deaminase-reductase involved in riboflavin biosynthesis

Biochemistry

Volumn 47, Issue 24, 2008, Pages 6499-6507

  Magalhães, Maria L B ^a   Argyrou, Argyrides ^a,b   Cahill, Sean M ^a   Blanchard, John S ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b BRISTOL MYERS SQUIBB   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION; AMINES; ARCHITECTURAL DESIGN; BIOCHEMICAL ENGINEERING; BIOCHEMISTRY; BIOSYNTHESIS; CHEMOTHERAPY; DRUG DELIVERY; DRUG DOSAGE; DRUG THERAPY; ESCHERICHIA COLI; MAMMALS; MICROFLUIDICS; TARGETS; THREE DIMENSIONAL;

BIFUNCTIONAL; DRUG DESIGNS; KINETIC (POLYM.); MECHANISTIC ANALYSIS; REDUCTASE (BVR-A); RIBOFLAVIN (RF); RIBOFLAVIN BIOSYNTHESIS; THREE-DIMENSIONAL (3D) STRUCTURING;

FOOD ADDITIVES;

DEAMINASE; OXIDOREDUCTASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; RIBOFLAVIN; RIBOSE;

ARTICLE; BIOSYNTHESIS; CATALYSIS; DEAMINATION; DRUG DESIGN; ESCHERICHIA COLI; GENE FUNCTION; KINETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN TRANSPORT; REDUCTION; RING OPENING; STRUCTURAL HOMOLOGY;

CATALYSIS; DEAMINATION; DEUTERIUM EXCHANGE MEASUREMENT; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; KINETICS; NADP; NUCLEOTIDE DEAMINASES; OXIDATION-REDUCTION; PENTOSEPHOSPHATES; PROTEIN STRUCTURE, TERTIARY; RIBOFLAVIN; SCHIFF BASES; SOLVENTS; SUBSTRATE SPECIFICITY; SUGAR ALCOHOL DEHYDROGENASES;

ESCHERICHIA COLI; MAMMALIA;

EID: 45749137952     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800264g     Document Type: Article

References (36)

1. Massey, V. (2000) The chemical and biological versatility of riboflavin. Biochem. Soc. Trans. 28, 283-296.
2. Bacher, A., Eberhardt, S., Fischer, M., Kis, K., and Richter, G. (2000) Biosynthesis of vitamin b2 (riboflavin). Annu. Rev. Nutr. 20, 153-167.
3. Bacher, A., Eberhardt, S., Eisenreich, W., Fischer, M., Herz, S., Illarionov, B., Kis, K., and Richter, G. (2001) Biosynthesis of riboflavin. Vitam. Horm. 61, 1-49.
4. Burgess, C. M., Slotboom, D. J., Geertsma, E. R., Duurkens, R. H., Poolman, B., and van Sinderen, D. (2006) The riboflavin transporter RibU in Lactococcus lactis: Molecular characterization of gene expression and the transport mechanism. J. Bacteriol. 188, 2752-2760.
5. Duurkens, R. H., Tol, M. B., Geertsma, E. R., Permentier, H. P., and Slotboom, D. J. (2007) Flavin binding to the high affinity riboflavin transporter RibU. J. Biol. Chem. 282, 10380-10386.
6. Mac, L. J. (1952) The effects of certain purines and pyrimidines upon the production of riboflavin by Eremothecium ashbyii. J. Bacteriol. 63, 233-241.
7. Oltmanns, O., and Bacher, A. (1972) Biosynthesis of riboflavine in Saccharomyces cerevisiae: The role of genes rib 1 and rib 7. J. Bacteriol. 110, 818-822.
8. Bacher, A., and Lingens, F. (1971) Biosynthesis of riboflavin. Formation of 6-hydroxy-2,4,5-triaminopyrimidine in rib 7 mutants of Saccharomyces cerevisiae. J. Biol. Chem. 246, 7018-7022.
9. Bacher, A., and Lingens, F. (1970) Biosynthesis of riboflavin. Formation of 2,5-diamino-6-hydroxy-4-(1′-D-ribitylamino)pyrimidine in a riboflavin auxotroph. J. Biol. Chem. 245, 4647-4652.
10. Richter, G., Ritz, H., Katzenmeier, G., Volk, R., Kohnle, A., Lottspeich, F., Allendorf, D., and Bacher, A. (1993) Biosynthesis of riboflavin: Cloning, sequencing, mapping, and expression of the gene coding for GTP cyclohydrolase II in Escherichia coli. J. Bacteriol. 175, 4045-4051.
11. Ritz, H., Schramek, N., Bracher, A., Herz, S., Eisenreich, W., Richter, G., and Bacher, A. (2001) Biosynthesis of riboflavin: Studies on the mechanism of GTP cyclohydrolase II. J. Biol. Chem. 276, 22273-22277.
12. Schramek, N., Bracher, A., and Bacher, A. (2001) Biosynthesis of riboflavin. Single turnover kinetic analysis of GTP cyclohydrolase II. J. Biol. Chem. 276, 44157-44162.
13. Ren, J., Kotaka, M., Lockyer, M., Lamb, H. K., Hawkins, A. R., and Stammers, D. K. (2005) GTP cyclohydrolase II structure and mechanism. J. Biol. Chem. 280, 36912-36919.
14. Richter, G., Fischer, M., Krieger, C., Eberhardt, S., Luttgen, H., Gerstenschlager, I., and Bacher, A. (1997) Biosynthesis of riboflavin: Characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis. J. Bacteriol. 179, 2022-2028.
15. Burrows, R. B., and Brown, G. M. (1978) Presence of Escherichia coli of a deaminase and a reductase involved in biosynthesis of riboflavin. J. Bacteriol. 136, 657-667.
16. Hollander, I., and Brown, G. M. (1979) Biosynthesis of riboflavin: Reductase and deaminase of Ashbya gossypii. Biochem. Biophys. Res. Commun. 89, 759-763.
17. Nielsen, P., and Bacher, A. (1981) Biosynthesis of riboflavin. Characterization of the product of the deaminase. Biochim. Biophys. Acta 662, 312-317.
18. Fischer, M., Romisch, W., Saller, S., Illarionov, B., Richter, G., Rohdich, F., Eisenreich, W., and Bacher, A. (2004) Evolution of vitamin B2 biosynthesis: Structural and functional similarity between pyrimidine deaminases of eubacterial and plant origin. J. Biol. Chem. 279, 36299-36308.
19. Stenmark, P., Moche, M., Gurmu, D., and Nordlund, P. (2007) The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: Implications for the reductive mechanism. J. Mol. Biol. 373, 48-64.
20. Chen, S. C., Chang, Y. C., Lin, C. H., and Liaw, S. H. (2006) Crystal structure of a bifunctional deaminase and reductase from Bacillus subtilis involved in riboflavin biosynthesis. J. Biol. Chem. 281, 7605-7613.
21. Keller, P. J., Le Van, Q., Kim, S. U., Bown, D. H., Chen, H. C., Kohnle, A., Bacher, A., and Floss, H. G. (1988) Biosynthesis of riboflavin: Mechanism of formation of the ribitylamino linkage. Biochemistry 27, 1117-1120.
22. Bresler, S. E., Glazunov, E. A., Perumov, D. A., and Chernik, T. P. (1977) Riboflavin biosynthesis Operon of Bacillus subtilis. XIII. Genetic and biochemical study of mutants with regard to intermediate stages of biosynthesis. Genetika 13, 2006-2016.
23. Mostad, S. B., Helming, H. L., Groom, C., and Glasfeld, A. (1997) The stereospecificity of hydrogen transfer to NAD(P)+ catalyzed by lactol dehydrogenases. Biochem. Biophys. Res. Commun. 233, 681-686.
24. Orr, G. A., and Blanchard, J. S. (1984) High-performance ion-exchange separation of oxidized and reduced nicotinamide adenine dinucleotides. Anal. Biochem. 142, 232-234.
25. Argyrou, A., Jin, L., Siconilfi-Baez, L., Angeletti, R. H., and Blanchard, J. S. (2006) Proteome-wide profiling of isoniazid targets in Mycobacterium tuberculosis. Biochemistry 45, 13947-13953.
26. Betts, L., Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W., Jr. (1994) Cytidine deaminase. The 2.3 Å crystal structure of an enzyme:transition-state analog complex. J. Mol. Biol. 235, 635-656.
27. Frick, L., Yang, C., Marquez, V. E., and Wolfenden, R. (1989) Binding of pyrimidin-2-one ribonucleoside by cytidine deaminase as the transition-state analogue 3,4-dihydrouridine and the contribution of the 4-hydroxyl group to its binding affinity. Biochemistry 28, 9423-9430.
28. Kati, W. M., and Wolfenden, R. (1989) Major enhancement of the affinity of an enzyme for a transition-state analog by a single hydroxyl group. Science 243, 1591-1593.
29. Kati, W. M., and Wolfenden, R. (1989) Contribution of a single hydroxyl group to transition-state discrimination by adenosine deaminase: Evidence for an "entropy trap" mechanism. Biochemistry 28, 7919-7927.
30. Kati, W. M., Acheson, S. A., and Wolfenden, R. (1992) A transition state in pieces: Major contributions of entropic effects to ligand binding by adenosine deaminase. Biochemistry 31, 7356-7366.
31. 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.
32. Miller, G. P., and Benkovic, S. J. (1998) Stretching exercises: Flexibility in dihydrofolate reductase catalysis. Chem. Biol. 5, R105-R113.
33. Yu, M., Magalhaes, M. L., Cook, P. F., and Blanchard, J. S. (2006) Bisubstrate inhibition: Theory and application to N-acetyltransferases. Biochemistry 45, 14788-14794.
34. Magalhaes, M. L., Vetting, M. W., Gao, F., Freiburger, L., Auclair, K., and Blanchard, J. S. (2008) Kinetic and structural analysis of bisubstrate inhibition of the Salmonella enlerica aminoglycoside 6′-N- acetyltransferase. Biochemistry 47, 579-584.
35. Morrison, J. F., and Stone, S. R. (1988) Mechanism of the reaction catalyzed by dihydrofolate reductase from Escherichia coli: pH and deuterium isotope effects with NADPH as the variable substrate. Biochemistry 27, 5499-5506.
36. Le Van, Q., Keller, P. J., Bown, D. H., Floss, H. G., and Bacher, A. (1985) Biosynthesis of riboflavin in Bacillus subtilis: Origin of the four-carbon moiety. J. Bacteriol. 162, 1280-1284.