Structure of L-aspartate oxidase: Implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family

Structure

Volumn 7, Issue 7, 1999, Pages 745-756

  Mattevi, Andrea ^a   Tedeschi, Gabriella ^b   Bacchella, Luca ^a   Coda, Alessandro ^a   Negri, Armando ^b   Ronchi, Severino ^b  

^a UNIVERSITY OF PAVIA   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

Catalysis; Flavin; L aspartate oxidase; NAD+ biosynthesis; Succinate dehydrogenase

Indexed keywords

AMINO ACID OXIDASE; BACTERIAL ENZYME; FUMARATE REDUCTASE; SUCCINATE DEHYDROGENASE;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME BINDING; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; STRUCTURE ANALYSIS;

EID: 0001406338     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80099-9     Document Type: Article

References (55)

1. Tritz, G.J. (1987). NAD biosynthesis and recycling. In Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology, Vol. 1. (Neidhart, F.C., Ingraham, J.L., Low, K.B., Magasanik, B., Schaechter, M. & Umbarger, H.E., eds.), pp. 557-563, American Society for Microbiology, Washington DC.
2. Foster, J.W. & Moat, A.G. (1980). Nicotinamide adenine dinucleotide biosynthesis and pyridine nucleotide cycle metabolism in microbial systems. Microbiol. Rev. 44, 83-105.
3. Penfound, T. & Foster, J.W. (1996). Biosynthesis and recycling of NAD. In Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology. 2nd Edn, (Neidhardt, F.C., ed.), pp. 721-730, American Society for Microbiology, Washington DC.
4. White, H.B. III. (1982). Biosynthetic and salvage pathways of pyridine nucleotides coenzymes. In The Pyridine Nucleotide Coenzymes. (Everse, J., Anderson, B.M. & You, K.-S., eds), pp. 225-248, Academic Press, NY, USA.
5. + synthetase from Bacillus subtilis. The EMBO J. 15, 5125-5134.
6. Eads, J.C., Ozturk, D., Wexler, T.B., Grubmeyer, C. & Sacchettini, J.C. (1997). A new function for a common fold: The crystal structure of quinolinic acid phosphoribosyltransferase. Structure 5, 47-58.
7. Griffith, G.R., Chandler, J.L.R. & Gholson, R.K. (1975). Studies on the de novo biosynthesis of nicotinamide adenine dinucleotide in Escherichia coli: The separation of the nadB gene product and its purification. Eur. J. Biochem. 175, 221-228.
8. Nasu, S., Wicks, F.D. & Gholson, R.K. (1982). L-aspartate oxidase, a newly discovered enzyme of Escherichia coli, is the B protein of quinolinate synthetase. J. Biol. Chem. 257, 626-632.
9. Seifert, J., Kunz, N., Flachmann, R., Laufer, A., Jany, K.-D. & Gassen, H.G. (1990). Expression of the E. coli nadB gene and characterization of the gene product L-aspartate oxidase. Biol. Chem. Hoppe-Seyler 371, 239-248.
10. Mortarino, M., et al., & Ronchi, S. (1996). L-aspartate oxidase from Escherichia coli. I. Characterization of coenzyme binding and product inhibition. Eur. J. Biochem. 239, 418-426.
11. Tedeschi, G., et al., & Ronchi, S. (1996). 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. 239, 427-433.
12. Tedeschi, G., Zetta, L., Negri, A., Mortarino, M., Ceciliani, F. & Ronchi, S. (1997). Redox potentials and quinone reductase activity of L-aspartate oxidase from Escherichia coli. Biochemistry 36, 16221-16230.
13. Ackrell, B.A., Johnson, M.K., Gunsalus, R.P. & Cecchini, G. (1991). Structure and function of succinate dehydrogenase and fumarate reductase. In Chemistry and Biochemistry of Flavoenzymes. (Müller, F., ed.), pp. 229-297, CRC Press, Boca Raton, FL.
14. Hägerhäll, C. (1997). Succinate: Quinone oxidoreductases. Variations on a conserved theme. Biochem. Biophys. Acta 1320, 107-141.
15. Mattevi, A., Fraaije, M.W., Mozzarelli, A., Olivi, L, Coda, A. & van Berkel, W.J.H. (1997). Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: The shape of the active-site cavity controls substrate specificity. Structure 5, 907-920.
16. Mattevi, A., Vanoni, M.A. & Curti, B. (1997). Structure of D-amino acid oxidase: New insights from an old enzyme. Curr. Opin. Struct. Biol. 7, 804-810.
17. + synthetase structure. Structure 6, 1129-1140.
18. Wierenga, R.K., Drenth, J. & Schulz, G.E. (1983). Comparison of the three-dimensional protein and nucleotide structure of the FAD-binding domain of p-hydroxybenzoate hydroxylase with the FAD as well as NADPH-binding domains of glutathione reductase. J. Mol. Biol. 167, 725-739.
19. de La Fortelle, E. & Bricogne, G. (1997). Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 442-494.
20. Brünger, A.T. (1992). Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
21. Tedeschi, G., Negri A., Ceciliani, F., Mattevi, A. & Ronchi, S. (1999). Structural characterisation of L-aspartate oxidase and identification of an interdomain loop by limited proteolysis. Eur. J. Biochem. 260, 896-903.
22. Lupas, A. (1996). Coiled coils: New structures and new functions. Trends Biosci. 21, 375-382.
23. Jones, S. & Thornton, J.M. (1995). Protein-protein interactions: A review of protein dimer interfaces. Prog. Biophys. Mol. Biol. 63, 31-65.
24. Holm, L & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
25. Bernstein, F.C., et al, & Tasumi, M. (1977). The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
26. Wierenga, R.K., Terpstra, P. & Hol W.G.J. (1986). Prediction of the occurrence of the ADP-binding βαβ-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol. 187, 101-107.
27. Waksman, G., Krishna, T.S.R., Williams C.H. Jr. & Kuriyan, J. (1994). Crystal structure of Escherichia coli thioredoxin reductase refined at 2 Å resolution. Implications for a large conformational change during catalysis. J. Mol. Biol. 236, 800-816.
28. Stehle, T., Ahmed, S.A., Claiborne, A. & Schulz, G.E. (1991). Structure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16 Å resolution. J. Mol. Biol. 221, 1325-1344.
29. Karplus, P.A. & Schulz, G.E. (1987). Refined structure of glutathione reductase at 1.54 Å resolution. J. Mol. Biol. 195, 701-729.
30. Chen, Z.-W., et al., & Mathews, F.S. (1994). The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Science 266, 430-432.
31. Hecht, HJ., Kalisz, H.M., Hendle, J., Schmid, R.D. & Schomburg, D. (1993). Crystal structure of glucose oxidase from Aspergillus niger refined at 2.3 Å resolution. J. Mol. Biol. 229, 153-172.
32. Schreuder, H.A., et al., & Drenth, J. (1989). Crystal structure of the p- hydroxybenzoate hydroxylase-substrate complex refined at 1.9 Å resolution. J. Mol, Biol. 208, 679-696.
33. Vrielink, A., Lloyd, L.F. & Blow, D.M. (1991). Crystal structure of cholesterol oxidase from Brevibacterium sterolicum refined at 1.8 Å resolution. J. Mol. Biol. 219, 533-554.
34. Schalk, I., et al., & Balch, W.E. (1996). Structure and mutational analysis of Rab GDP-dissociation inhibitor. Nature 381, 42-48.
35. 2. Proc. Natl Acad. Sci. USA 93, 7496-7501.
36. Mizutani, H., et al., & Miura, R. (1996). Three-dimensional structure of porcine kidney D-amino acid oxidase at 3 Å resolution. J. Biochem. 120, 14-17.
37. Lim, L.W., Shamal, N., Mathews, F.S., Steenkamp, D.J., Hamlin, R. & Xuong, N. (1986). Three-dimensional structure of the iron-sulphur flavoprotein trimethylamine dehydrogenase at 2.4 Å resolution. J. Biol. Chem. 261, 15140-15146.
38. Mattevi, A. (1997). The PHBH fold: Not only flavoenzymes. Biophys. Chem. 70, 21 7-222.
39. Pai, E.F. (1991). Variations on a theme: The family of FAD-dependent NAD(P)H-(disulphide)-oxidoreductases. Curr. Opin. Struct. Biol. 1, 796-803.
40. lactose from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system. Structure 5, 775-788.
41. Andersson, I. (1996). Large structures at high resolution: The 1.6 Å crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate. J. Mol. Biol. 259, 160-174.
42. Ghisla, S. & Massey, V. (1989). Mechanisms of flavoprotein-catalyzed reactions. Eur. J. Biochem. 181, 1-17.
43. Vik, S.B. & Hatefi, Y. (1981 ). Possible occurrence and role of an essential histidyl residue in succinate dehydrogenase. Proc. Natl Acad Sci. USA 78, 6749-6753.
44. Schröder, I., Gunsalus, R.P., Ackrell, B.A.C., Cochran, B. & Cecchini, G. (1991 ). Identification of active site residues of Escherichia coli fumarate reductase by site-directed mutagenesis. J. Biol. Chem. 266, 13572-13579.
45. Bacchella, L., et al., & Mattevi, A. (1999). Crystallisation of L-aspartate oxidase, the first enzyme in the bacterial de novo biosynthesis of NAD. Acta Crystallogr. D 55, 549-551.
46. Collaborative Computational Project Number (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-767.
47. 1 ATPase. Acta Crystallogr. D 52, 30-42.
48. Jones, TA, Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
49. Perrakis, A., Morris, R. & Lamzin, V. (1999). Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458-463.
50. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255.
51. Lamzin, V. & Wilson, K.S. (1993). Automated refinement of protein models. Acta Crystallogr. D 49, 129-147.
52. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: A program to check the stereochemistry of protein structures. J. Appl. Crystallogr. 26, 283-291.
53. Kleywegt, G.J. & Jones, T.A. (1994). Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D 50, 178-185.
54. Kraulis, P.J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
55. Esnouf, R.M. (1999). Further additions to MolScript version 1.4, including reading and contouring of electron density maps. Acta Crystallogr. D 55, 938-940.