Discovery and characterization of d-phenylserine deaminase from Arthrobacter sp. TKS1
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.
Từ khóa
Tài liệu tham khảo
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