Homologous gene clusters of nicotine catabolism, including a new ω-amidase for α-ketoglutaramate, in species of three genera of Gram-positive bacteria

Research in Microbiology

Volumn 162, Issue 3, 2011, Pages 285-291

  Cobzaru, Cristina ^a   Ganas, Petra ^a   Mihasan, Marius ^b   Schleberger, Paula ^a   Brandsch, Roderich ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b ALEXANDRU IOAN CUZA UNIVERSITY OF IASI   (Romania)

Author keywords

amidase; Arthrobacter nicotinovorans; Nicotine catabolism; Nocardioides sp. JS614; PAO1; Rhodococcus opacus

Indexed keywords

2 OXOGLUTARAMIC ACID; 2,6 DIHYDROXYPYRIDINE; AMIDASE; CARBON; DICARBOXYLIC AMINO ACID; GLUTAMIC ACID; MALEAMATE; NICOTINE; NITRILASE; NITROGEN; OMEGA AMIDASE; PYRIDINE DERIVATIVE; TRIHYDROXYPYRIDINE; UNCLASSIFIED DRUG;

ARTHROBACTER; ARTHROBACTER NICOTINOVORANS; ARTICLE; BACTERIAL GENE; CATABOLISM; CHEMICAL BOND; ENZYME ACTIVITY; ENZYME STRUCTURE; GENE CLUSTER; GRAM POSITIVE BACTERIUM; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROLYSIS; NITROGEN METABOLISM; NOCARDIOIDES; NONHUMAN; PIMELOBACTER; PRIORITY JOURNAL; PROTEIN PURIFICATION; RHODOCOCCUS; RHODOCOCCUS OPACUS;

ACTINOMYCETALES; AMIDOHYDROLASES; ARTHROBACTER; CATALYTIC DOMAIN; GENE ORDER; KETOGLUTARIC ACIDS; METABOLIC NETWORKS AND PATHWAYS; MODELS, MOLECULAR; MULTIGENE FAMILY; NICOTINE; PROTEIN STRUCTURE, TERTIARY; RHODOCOCCUS;

ARTHROBACTER NICOTINOVORANS; NOCARDIOIDES SP.; POSIBACTERIA; RHODOCOCCUS OPACUS;

EID: 79952898929     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2011.01.001     Document Type: Article

References (32)

1. Agarkar V.B., Kimani S.W., Cowan D.A., Sayed MF.-R., Sewell B.T. The quaternary structure of the amidase from Geobacillus pallidus rapc8 is revealed by its crystal packing. Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 2006, 62:1174-1178.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
3. Arnold K., Bordoli L., Kopp J., Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22:195-201.
4. Behrman E.J., Stanier R.Y. Observations on the oxidation of halogenated nicotinic acids. J. Biol. Chem. 1957, 228:923-945.
5. Berthold H., Sacarini M., Abney C.C., Frorath B., Northemann W. Purification of recombinant antigenic epitopes of the human 68-kDa (U1) ribonucleoprotein antigen using the expression system pH6EX3 followed by metal chelating affinity chromatography. Protein Expr. Purif. 1992, 3:50-56.
6. Bönicke R., Ewoldt A., Röhrscheid E. Untersuchungen über die induktive Nicotinsäurehydroxylase-Bildung bei Mycobacterium smegmatis. Pneumonologie 1970, 142:173-181.
7. Brandsch R. Microbiology and biochemistry of nicotine degradation. Appl. Microbiol. Biotechnol. 2006, 69:493-498.
8. Brenner C. Catalysis in the nitrilase superfamily. Cur. Opin. Struc. Biol. 2002, 12:775-782.
9. Brühmüller M., Möhler H., Decker K. Covalently bound flavin in D-6-hydroxynicotine oxidase from Arthrobacter oxidans. Purification and properties of D-6-hydroxynicotine oxidase. Eur. J. Biochem. 1972, 29:143-151.
10. Dundas J., Ouyang Z., Tseng J., Binkowski A., Turpaz Y., Liang J. Castp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res. 2006, 34:W116-W118.
11. Ganas P., Sachelaru P., Mihasan M., Igloi G.L., Brandsch R. Two closely related pathways of nicotine catabolism in Arthrobacter nicotinovorans and Nocardioides sp. strain JS614. Arch. Mikrobiol. 2008, 189:511-517.
12. Gauthier J.J., Rittenberg S.C. The metabolism of nicotinic acid. II. 2,5-dihydroxypyridine oxidation, product formation, and oxygen 18 incorporation. J. Biol. Chem. 1971, 246:3743-3748.
13. Goto M., Omi R., Miyahara I., Hosono A., Mizuguchi H., Hayashi H., Kagamiyama H., Hirotsu K. Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8. J. Biol. Chem. 2004, 279:16518-16525.
14. Hosono A., Mizuguchi H., Hayashi H., Goto M., Miyahara I., Hirotsu K., Kagamiyama H. Glutamine:phenylpyruvate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus HB8. J. Biochem. 2003, 134:843-851.
15. Igloi G.L., Brandsch R. Sequence of the 165-kilobase catabolic plasmid pAO1 from Arthrobacter nicotinovorans and identification of a pAO1-dependent nicotine uptake system. J. Bacteriol. 2003, 185:1976-1989.
16. Jaisson S., Veiga-da-Cubha M., Van Schafting E. Molecular identification of omega-amidase, the enzyme that is functionally coupled with glutamine transaminases, as the putative tumor suppressor Nit2. Biochemie 2009, 91:1066-1071.
17. Jiménez J.I., Canales A., Jiménez-Barbero J., Ginalski K., Rychlewski L., Gracia J.L., Díaz E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc. Nat. Acad. Sienc. USA 2008, 105:11329-11334.
18. Kimani S.W., Agarkar V.B., Cowan D.A., Sayed MF.-R., Sewell B.T. Structure of an aliphatic amidase from Geobacillus pallidus rapc8. Acta Crystallogr. D. Biol. Crystallogr. 2007, 63:1048-1058.
19. Krasnikov B.F., Nostramo R., Pinto J.T., Cooper A.J.L. Assay and purification of omega-amidase/Nit2, a ubiquitously expressed putative tumor suppressor, that catalyzis the deamidation of the aplpha-keto acid analogues of glutamine and asparagine. Anal. Biochem. 2009, 391:144-150.
20. Krasnikov B.F., Chien C.H., Nostramo R., Pinot J.T., Nieves E., Callaway M., Sun J., Huebner K., Cooper A.J. Identification of the putative tumor suppressor Nit2 as omega-amidase, an enzyme metabolically linked to glutamine and asparagine transamination. Biochemie 2009, 91:1972-1980.
21. Lakowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. {PROCHECK}: a program to check the stereochemical quality of protein structures. J. Appl. Cryst 1993, 26:283-291.
22. Lang P.T., Brozell S.R., Mukherjee S., Pettersen E.F., Meng E.C., Thomas V., Rizzo R.C., Case D.A., James T.L., Kuntz I.D. Dock 6: combining techniques to model RNA-small molecule complexes. RNA 2009, 15:1219-1230.
23. Makhongela H.S., Glowacka A.E., Agarkar V.B., Sewell B.T., Weber B., Cameron R.A., Cowan D.A., Burton S.G. A novel thermo stable nitrilase superfamily amidase from Geobacillus pallidus showing acyl transfer activity. Appl. Microbiol. Biotechnol. 2007, 75:801-811.
24. Meister A., Levintow R.E., Greenfield P.A., Abendschein P.A. Hydrolysis and transfer reactions catalyzed by ω-amidase preparations. J. Biol. Chem. 1955, 215:441-460.
25. Neumann M., Stöcklein W., Leimkühler S. Transfer of the molybdenum cofactor synthesized by Rhodobacter capsulatus MoeA to XdhC and MobA. J. Biol. Chem. 2007, 282:28493-28500.
26. Otani T.T., Meister A. ω-Amide and ω-amino acid derivatives of α-ketoglutaric acid and oxalacetic acids. J. Biol. Chem. 1957, 224:137-148.
27. Pace H.C., Brenner C. The nitrilase superfamily: classification, structure and function. GenomeBiology 2001, 2:1-9.
28. 2] cluster. J. Biol. Chem. 2009, 284:9578-9586.
29. Pettersen E.F., Goddard T.D., Huang C.C., Souch C.G., Greenblatt D.M., Meng E.C., Ferrin T.E. Ucsf chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
30. Schwarz G., Mendel R.R., Ribbe M.W. Molybdenum cofactors, enzymes and pathways. Nature 2009, 460:839-847.
31. Tang H., Wang S., Ma L., Meng X., Deng Z., Zhang D., Ma C., Xu P. A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida Strain S16. App Environ. Microbiol. 2008, 74:1567-1574.
32. Zefirov N.S., Agapova S.R., Terentiev P.B., Bulakhova I.M., Vasyukova N.I., Modyanova L.V. Degradation of pyridine by Arthrobacter crystallopoietes and Rhodococcus opacus strains. FEMS Microbiol. Lett. 1994, 188:71-74.