Discovery and characterization of d-phenylserine deaminase from Arthrobacter sp. TKS1

Hisashi Muramatsu1, Yuri Suzuki2, Takeshi Imai3,4, Sakuko Ueshima4, Jun Ozaki5, Yuji Matsui5, Shin-ichiro Kato1, Kouhei Ohnishi1, Norihiro Kimoto6, Hiroaki Yamamoto6, Shinji Nagata1
1Multidisciplinary Science Cluster, Research and Education Faculty, Kochi University, Nankoku, Japan
2Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
3Institute for Chemical Research, Kyoto University, Uji, Japan
4Department of Bioresources Science, Faculty of Agriculture, Kochi University, Nankoku, Japan
5Life Chemistry Course, Faculty of Agriculture, Kochi University, Nankoku, Japan
6Corporate Research Center, Daicel Chemical Industries, Ltd., Himeji, Japan

Tóm tắt

We discovered a d-phenylserine deaminase that catalyzed the pyridoxal 5′-phosphate (PLP)-dependent deamination reaction from d-threo-phenylserine to phenylpyruvate in newly isolated Arthrobacter sp. TKS1. The enzyme was partially purified, and its N-terminal amino acid sequence was analyzed. Based on the sequence information, the gene encoding the enzyme was identified and expressed in Escherichia coli. The expressed protein was purified to homogeneity and characterized. The enzyme consisted of two identical 46-kDa subunits and showed maximum activity at pH 8.5 and 55°C. The enzyme was stable in the range of pH 7.5 to pH 8.5 and up to 50°C. The enzyme acted on the d-forms of β-hydroxy-α-amino acids, such as d-threo-phenylserine (K m, 19 mM), d-serine (K m, 5.8 mM), and d-threonine (K m, 102 mM). As l-threonine, d-allo-threonine, l-allo-threonine, and dl-erythro-phenylserine were inert, the enzyme could distinguish d-threo-form from among the four stereoisomers of phenylserine or threonine. The enzyme was activated by ZnSO4, CuSO4, BaCl2, and CoCl2 and strongly inhibited by phenylhydrazine, sodium borohydride, hydroxylamine, and dl-penicillamine. The enzyme exhibited absorption maxima at 280 and around 415 nm. The enzyme has an N-terminal domain similar to that of alanine racemase, which belongs to the fold type III group of pyridoxal enzymes.

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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A (2008) The Pfam protein families database. Nucleic Acids Res 36:D281–D288 Foltyn VN, Bendikov I, De Miranda J, Panizzutti R, Dumin E, Shleper M, Li P, Toney MD, Kartvelishvily E, Wolosker H (2005) Serine racemase modulates intracellular D-serine levels through an α, β-elimination activity. J Biol Chem 280:1754–1763 Gokulan K, Rupp B, Pavelka MS Jr, Jacobs WR Jr, Sacchettini JC (2003) Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis. J Biol Chem 278:18588–18596 Grishin NV, Phillips MA, Goldsmith EJ (1995) Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci 4:1291–1304 Grishin NV, Osterman AL, Brooks HB, Phillips MA, Goldsmith EJ (1999) X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with α-difluoromethylornithine. Biochemistry 38:15174–15184 Haraguchi K, Mori S, Hayashi K (2000) Cloning of inulin fructotransferase (DFA III-producing) gene from Arthrobacter globiformis C11-1. J Biosci Bioeng 89:590–595 Hayashi H, Inoue K, Mizuguchi H, Kagamiyama H (1996) Analysis of the substrate-recognition mode of aromatic amino acid aminotransferase by combined use of quasisubstrates and site-directed mutagenesis: systematic hydroxy-group addition/deletion studies to probe the enzyme–substrate interactions. Biochemistry 35:6754–6761 Ito T, Hemmi H, Kataoka K, Mukai Y, Yoshimura T (2008) A novel zinc-dependent D-serine dehydratase from Saccharomyces cerevisiae. Biochem J 409:399–406 Kataoka M, Ikemi M, Morikawa T, Miyoshi T, Nishi K, Wada M, Yamada H, Shimizu S (1997) Isolation and characterization of D-threonine aldolase, a pyridoxal-5′-phosphate-dependent enzyme from Arthrobacter sp. DK-38. Eur J Biochem 248:385–393 Kikuchi J, Takashima T, Nakao H, Hie K, Etoh H, Noguchi Y, Suehiro K, Murakami Y (1993) Stereoselective synthesis of β-phenylserine from glycine and benzaldehyde as mediated by catalytic bilayer membranes, artificial vitamin B6-dependent enzymes. Chem Lett 1993:553–556 Liu JQ, Ito S, Dairi T, Itoh N, Kataoka M, Shimizu S, Yamada H (1998a) Gene cloning, nucleotide sequencing, and purification and characterization of the low-specificity L-threonine aldolase from Pseudomonas sp. strain NCIMB 10558. Appl Environ Microbiol 64:549–554 Liu JQ, Ito S, Dairi T, Itoh N, Shimizu S (1998b) Low-specificity L-threonine aldolase of Pseudomonas sp. NCIMB 10558: purification, characterization and its application to β-hydroxy-α-amino acid synthesis. Appl Microbiol Biotechnol 49:702–708 Liu JQ, Dairi T, Itoh N, Kataoka M, Shimizu S, Yamada H (1998c) A novel metal-activated pyridoxal enzyme with a unique primary structure, low specificity D-threonine aldolase from Arthrobacter sp. strain DK-38. Molecular cloning and cofactor characterization. J Biol Chem 273:16678–16685 Liu JQ, Dairi T, Itoh N, Kataoka M, Shimizu S, Yamada H (1998d) Gene cloning, biochemical characterization and physiological role of a thermostable low-specificity L-threonine aldolase from Escherichia coli. FEBS J 255:220–226 Liu JQ, Dairi T, Itoh N, Kataoka M, Shimizu S (2003) A novel enzyme, D-3-hydroxyaspartate aldolase from Paracoccus denitrificans IFO 13301: purification, characterization, and gene cloning. Appl Microbiol Biotechnol 62:53–60 Lowry CH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193:265–275 Maeda T, Takeda Y, Murakami T, Yokota A, Wada M (2010) Purification, characterization, and amino acid sequence of a novel enzyme, D-threo-3-hydroxyaspartate dehydratase, from Delftia sp. HT23. J Biochem. doi:10.1093/jb/mvq106 Marceau M, McFall E, Lewis SD, Shafer JA (1988) D-Serine dehydratase from Escherichia coli. DNA sequence and identification of catalytically inactive glycine to aspartic acid variants. J Biol Chem 263:16926–16933 Marceau M, Lewis SD, Kojiro CL, Shafer JA (1990) Disruption of active site interactions with pyridoxal 5′-phosphate and substrates by conservative replacements in the glycine-rich loop of Escherichia coli D-serine dehydratase. J Biol Chem 265:20421–20429 Mauch L, Bichler V, Brandsch R (1990) Functional analysis of the 5′ regulatory region and the UUG translation initiation codon of the Arthrobacter oxidans 6-hydroxy-D-nicotine oxidase gene. Mol Gen Genet 221:427–434 Mihara H, Muramatsu H, Kakutani R, Yasuda M, Ueda M, Kurihara T, Esaki N (2005) N-Methyl-L-amino acid dehydrogenase from Pseudomonas putida. A novel member of an unusual NAD(P)-dependent oxidoreductase superfamily. FEBS J 272:1117–1123 Misono H, Kato I, Packdibamrung K, Nagata S, Nagasaki S (1993) NADP+-dependent D-threonine dehydrogenase from Pseudomonas cruciviae IFO 12047. Appl Environ Microbiol 59:2963–2968 Misono H, Maeda H, Tuda K, Ueshima S, Miyazaki N, Nagata S (2005) Characterization of an inducible phenylserine aldolase from Pseudomonas putida 24-1. Appl Environ Microbiol 71:4602–4609 Miyazaki SS, Toki S, Izumi Y, Yamada H (1987) Purification and characterization of a serine hydroxymethyltransferase from an obligate methylotroph, Hyphomicrobium methylovorum GM2. Eur J Biochem 162:533–540 Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ (2006) Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet 2:e214 Muramatsu H, Mihara H, Kakutani R, Yasuda M, Ueda M, Kurihara T, Esaki N (2005) The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent Δ 1-piperideine-2-carboxylate/Δ 1-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-proline. J Biol Chem 280:5329–5335 Okuda H, Nagata S, Misono H (1996) A novel phenylserine dehydratase from Pseudomonas pickettii PS22: purification, characterization, and sequence of its phosphopyridoxyl peptide. J Biochem 119:690–696 Okuda H, Nagata S, Misono H (2002) Cloning, sequencing, and overexpression in Escherichia coli of a phenylserine dehydratase gene from Ralstonia pickettii PS22. Biosci Biotechnol Biochem 66:2755–2758 Packdibamrung K, Misono H, Harada M, Nagata S, Nagasaki S (1993) An inducible NADP+-dependent D-phenylserine dehydrogenase from Pseudomonas syringae NK-15: purification and biochemical characterization. J Biochem 114:930–935 Phillips RS, Parniak MA, Kaufman S (1984) The interaction of aromatic amino acids with rat liver phenylalanine hydroxylase. J Biol Chem 259:271–277 Rytka J (1975) Positive selection of general amino acid permease mutants in Saccharomyces cerevisiae. J Bacteriol 121:562–570 Schirch V, Hopkins S, Villar E, Angelaccio S (1985) Serine hydroxymethyltransferase from Escherichia coli: purification and properties. J Bacteriol 163:1–7 Shaw JP, Petsko GA, Ringe D (1997) Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9 Å resolution. Biochemistry 36:1329–1342 Shimizu Y, Sakuraba H, Kawakami R, Goda S, Kawarabayasi Y, Ohshima T (2005) L-Threonine dehydrogenase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3: gene cloning and enzymatic characterization. Extremophiles 9:317–324 Szebenyi DM, Musayev FN, di Salvo ML, Safo MK, Schirch V (2004) Serine hydroxymethyltransferase: role of glu75 and evidence that serine is cleaved by a retroaldol mechanism. Biochemistry 43:6865–6876 Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680 Ueshima S, Muramatsu H, Nakajima T, Yamamoto H, Kato S, Misono H, Nagata S (2010) Identification, cloning and characterization of L-phenylserine dehydrogenase from Pseudomonas syringae NK-15. Enzyme Research. 10.4061/2010/597010 Ulevitch RJ, Kallen RG (1977) Purification and characterization of pyridoxal 5′-phosphate dependent serine hydroxymethylase from lamb liver and its action upon β-phenylserines. Biochemistry 16:5342–5349 Villegas A, Kropinski AM (2008) An analysis of initiation codon utilization in the Domain Bacteria—concerns about the quality of bacterial genome annotation. Microbiology 154:2559–2661 Yow GY, Uo T, Yoshimura T, Esaki N (2006) Physiological role of D-amino acid-N-acetyltransferase of Saccharomyces cerevisiae: detoxification of D-amino acids. Arch Microbiol 185:39–46