Gene organization and molecular modeling of copper amine oxidase from Aspergillus niger: Re-evaluation of the cofactor structure

Biological Chemistry

Volumn 384, Issue 10-11, 2003, Pages 1451-1461

  Frébort, Ivo ^a   Šebela, Marek ^a   Hirota, Shun ^b   Yamada, Mamoru ^c   Tamaki, Hisanori ^d   Kumagai, Hidehiko ^d   Adachi, Osao ^c   Peč, Pavel ^a  

^a PALACKÝ UNIVERSITY   (Czech Republic)

^b KYOTO PHARMACEUTICAL UNIVERSITY   (Japan)

^c YAMAGUCHI UNIVERSITY   (Japan)

^d KYOTO UNIVERSITY   (Japan)

Author keywords

Fungi; Quinoprotein; Resonance Raman; Sequence; Topa quinone

Indexed keywords

AMINE OXIDASE (COPPER CONTAINING); COMPLEMENTARY DNA; GLUTAMIC ACID; HISTIDINE; PHENYLHYDRAZINE DERIVATIVE; QUINONE DERIVATIVE; REGULATOR PROTEIN;

ANALYTICAL ERROR; ASPERGILLUS NIGER; BINDING SITE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA SEQUENCE; ENZYME ISOLATION; ENZYME STRUCTURE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC ORGANIZATION; MOLECULAR CLONING; MOLECULAR MODEL; NEUROSPORA CRASSA; NITROGEN METABOLISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RAMAN SPECTROMETRY; REVIEW; SEQUENCE HOMOLOGY;

AMINE OXIDASE (COPPER-CONTAINING); AMINO ACID SEQUENCE; ASPERGILLUS NIGER; BASE SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; CLONING, MOLECULAR; COENZYMES; DIHYDROXYPHENYLALANINE; DNA, COMPLEMENTARY; GENES; GLUTAMIC ACID; HISTIDINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NEUROSPORA CRASSA; PHENYLHYDRAZINES; SEQUENCE ALIGNMENT; SPECTRUM ANALYSIS, RAMAN;

ASPERGILLUS; ASPERGILLUS NIGER; FUNGI; NEUROSPORA; NEUROSPORA CRASSA;

EID: 18544406091     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: 10.1515/BC.2003.161     Document Type: Review

References (42)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST. a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Brown, D.E., McGuirl, M.A., Dooley, D.M., Janes, S.M., Mu, D., and Klinman, J.P. (1991). The organic functional group in copper-containing amine oxidases. Resonance Raman spectra are consistent with the presence of topa quinone (6-hydroxydopa quinone) in the active site. J. Biol. Chem. 266, 4049-4051.
3. Bruinenberg, P.G., Evers, M., Waterham, H.R., Kuipers, J., Arnberg, A.C., and Ab, G. (1989). Cloning and sequencing of the peroxisomal amine oxidase gene from Hansenula polymorpha. Biochim. Biophys. Acta 1008, 157-167.
4. Cai, D.Y., Williams, N.K., and Klinman, J.P. (1997). Effect of metal on 2,4,5-trihydroxyphenylalanine (topa) quinone biogenesis in the Hansenula polymorpha copper amine oxidase. J. Biol. Chem. 272, 19277-19281.
5. Calderon, J., and Martinez, L.M. (1993). Regulation of ammonium ion assimilation enzymes in Neurospora crassa nit-2 and ms-5 mutant strains. Biochem. Genet. 31, 425-439.
6. Cooper, R.A., Knowles, P.F., Brown, D.E., McGuirl, M.A., and Dooley, D.M. (1992). Evidence for copper and 3,4,6-trihydroxyphenylalanine quinone cofactors in an amine oxidase from the gram-negative bacterium Escherichia coli K-12. Biochem. J. 288, 337-340.
7. Croft, L., Schandorff, S., Clark, F., Burrage, K., Arctander, P., Mattick, J.S. (2000). ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nature Genet. 24, 340-341.
8. Frébort, I., Peč, P., Luhová, L., Matsushita, K., Toyama, H., Adachi, O. (1994). Active-site covalent modifications of quinoprotein amine oxidases from Aspergillus niger. Evidence for binding of the mechanism-based inhibitor, 1,4-diamino-2-butyne, to residue Lys356 involved in the catalytic cycle. Eur. J. Biochem. 225, 959-965.
9. Frébort, I. and Adachi, O. (1995). Copper/quinone-containing amine oxidases, an exciting class of ubiquitous enzymes. J. Ferment. Bioeng. 80, 625-632.
10. Frébort, I., Tamaki, H., Ishida, H., Peč, P., Luhová, L., Tsuno, H., Halata, M., Asano, Y., Kato, Y., Matsushita, K., Toyama, H., Kumagai, H., and Adachi, O. (1996a). Two distinct quinoprotein amine oxidases are induced by n-butylamine in the mycelia of Aspergillus niger AKU 3302. Purification, characterization, cDNA cloning and sequencing. Eur. J. Biochem. 237, 255-265.
11. Frébort, I., Peč, P., Luhová, L., Toyama, H., Matsushita, K., Hirota, S., Kitagawa, T., Ueno, T., Asano, Y., Kato, Y., and Adachi, O. (1996b). Two amine oxidases from Aspergillus niger AKU 3302 contain topaquinone as the cofactor: unusual cofactor link to the glutamyl residue occurs only at one of the enzymes. Biochim. Biophys. Acta 1295, 59-72.
12. Frébort, I., Matsushita, K., Toyama, H., Lemr, K., Yamada, M., and Adachi, O. (1999). Purification and characterization of methylamine oxidase induced in Aspergillus niger AKU 3302. Biosci. Biotechnol. Biochem. 63, 125-134.
13. Frébort, I., Tanaka, S., Matsushita, K., and Adachi, O. (2000). Cellular localization and metabolic function of n-butylamine induced amine oxidases in the fungus Aspergillus niger AKU 3302. Arch. Microbiol. 173, 358-365.
14. Fu, Y.-H., and Marzluf, G.A. (1990). Nit-2, the major positive-acting nitrogen regulatory gene of Neurospora crassa, encodes a sequence-specific DNA-binding protein. Proc. Natl. Acad. Sci. USA 87, 5331-5335.
15. Guex, N., and Peitsch, M.C. (1997). SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis 18, 2714-2723.
16. Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucl. Acids Symp. Ser. 41, 95-98.
17. Hirota, S., Iwamoto, T., Tanizawa, K., Adachi, O., and Yamauchi, O. (1999). Spectroscopic characterization of carbon monoxide complexes generated for copper/topa quinone-containing amine oxidases. Biochemistry 38, 14256-14263.
18. Janes, S.M., Mu, D., Wemmer, D., Smith, A.J., Kaur, S., Maltby, D., Burlingame, A.L., and Klinman, J.P. (1990). A new redox cofactor in eukaryotic enzymes: 6-hydroxydopa at the active site of bovine serum amine oxidase. Science 248, 981-987.
19. Janes, S.M., Palcic, M.M., Scaman, C.H., Smith, A.J., Brown, D.E., Dooley, D.M., Mure, M., and Klinman, J.P. (1992). Identification of topaquinone and its consensus sequence in copper amine oxidases. Biochemistry 31, 12147-12154.
20. Kim, M., Okajima, T., Kishishita, S., Yoshimura, M., Kawamori, A., Tanizawa, K., Yamaguchi, H. (2002). X-ray snapshots of quinone cofactor biogenesis in bacterial copper amine oxidase. Nature Struct. Biol. 9, 591-596.
21. Kumar, V., Dooley, D.M., Freeman, H.C., Guss, J.M., Harvey, I., McGuirl, M.A., Wilce, M.C., Zubak, V.M. (1996). Crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2 Å resolution. Structure 4, 943-955.
22. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993). PROCHECK: a program to check the stereo-chemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
23. Li, R., Klinman, J.P., and Mathews, F. S. (1998). Copper amine oxidase from Hansenula polymorpha: the crystal structure determined at 2.4 Å resolution reveals the active site conformation. Structure 6, 293-307.
24. Maniatis, T., Sambrook, J., and Fritsch, E.F. (1989). Molecular Cloning: A Laboratory Manual. 2nd Edition (Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press).
25. Marchler-Bauer, A., Panchenko, A.R., Shoemaker, B.A., Thiessen, P.A., Geer, L.Y., and Bryant, S.H. (2002). CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30, 281-283.
26. Melville, C.R., Green, E.L., Sanders-Loehr, J., and Klinman, J.P. (2000). Reassessment of the active site quino-cofactor proposed to occur in the Aspergillus niger amine oxidase AO-I from the properties of model compounds. Biochemistry 39, 7589-7594.
27. Milanesi, L., D'Angelo, D., and Rogozin, I.B. (1999). GeneBuilder: interactive in silico prediction of genes structure. Bioinformatics 15, 612-621.
28. Moënne-Loccoz, P., Nakamura, N., Steinebach, V., Duine, J. A., Mure, M., Klinman, J. P., and Sanders-Loehr, J. (1995). Characterization of the topa quinone cofactor in amine oxidase from Escherichia coli by resonance Raman spectroscopy. Biochemistry 34, 7020-7026.
29. Nakamura, N., Matsuzaki, R., Choi, Y.H., Tanizawa, K., and Sanders-Loehr, J. (1996). Biosynthesis of topa quinone cofactor in bacterial amine oxidases. Solvent origin of C-2 oxygen determined by Raman spectroscopy. J. Biol. Chem. 271, 4718-4724.
30. Nakamura, N., Moënne-Loccoz, P., Tanizawa, K., Mure, M., Suzuki, S., Klinman, J. P., and Sanders-Loehr, J. (1997). Topaquinone-dependent amine oxidases: identification of reaction intermediates by Raman spectroscopy. Biochemistry 36, 11479-11486.
31. Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997). Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1-6.
32. Ohler, U., Harbeck S., Niemann H., Noeth, E., and Reese, M.G. (1999). Interpolated Markov chains for eukaryotic promoter recognition. Bioinformatics 15, 362-369.
33. Parsons, M.R., Convery, M.A., Wilmot, C.M., Yadav, K.D., Blakeley, V., Corner, A.S., Phillips, S.E., McPherson, M.J., Knowles, P.F. (1995). Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 Å resolution. Structure 3, 1171-1184.
34. Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T. (1995). MatInd and MatInspector-new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 23, 4878-4884.
35. Radloff, R., Bauer, W., and Vinograd, J. (1967). A dye-buoyant-density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells. Proc. Natl. Acad. Sci. USA 57, 1514-1521.
36. Tamaki, H., Ishida, H., Tsuno, H., Yamamoto, K., Adachi, O., and Kumagai, H. (1995). Amine oxidase from Aspergillus niger: cDNA cloning and expression in the yeast Saccharomyces cerevisiae. Biofactors 5, 45.
37. Tao, Y., and Marzluf, G.A. (1999). The NIT2 nitrogen regulatory protein of Neurospora: expression and stability of nit-2 mRNA and protein. Curr. Genet. 36, 153-158.
38. 6 binuclear cluster DNA binding motif. Fungal Genet. Biol. 21, 388-405.
39. van Aalten, D.M.F., Bywater, R., Findlay, J.B.C., Hendlich, M., Hooft, R.W.W., and Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aid. Mol. Design 10, 255-262.
40. van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P., Tironi, I.G. (1996). Biomolecular Simulation: The GROMOS96 Manual and User Guide (Zürich, Switzerland: Vdf Hochschulverlag AG/ETH Zürich).
41. Wang, S.X., Mure, M., Medzihradszky, K.F., Burlingame, A.L., Brown, D.E., Dooley, D.M., Smith, A.J., Kagan, H.M., and Klinman, J.P. (1996). A crosslinked cofactor in lysyl oxidase: redox function for amino acid side chains. Science 273, 1078-1084.
42. Xiao, X., and Marzluf, G.A. (1996). Identification of the native NIT2 major nitrogen regulatory protein in nuclear extracts of Neurospora crassa. Genetica 97, 153-163.