Alanine Racemase 5.1.1.1

Alanine racemase 5.1.1.1

1 Nomenclature

EC number 5.1.1.1 Systematic name Alanine racemase Recommended name Alanine racemase Synonyms l-Alanine racemase l-Alanine:D-alanine racemase Racemase, alanine CAS registry number 9024-06-0

2 Source Organism

<1> Streptococcus faecalis (O-carbamoyl-d-Ser-resistant mutant [6]) [1,6,24] <2> Bacillus subtilis [2,3,10,24] <3> Salmonella typhimurium (overproducing strain [7]; encoded by the dadB and alr gene [11]; encoded by alr and dadB gene [14]) [4,5,7,10,11,14,15, 24,31] <4> Bacillus stearothermophilus [8-12,14-18,20,21,23-25,30] <5> Pseudomonas aeruginosa (strain A237) [13] <6> Staphylococcus sp. [14] <7> E. coli (strain B [28]) [14,22,28,29] <8> Pseudomonas fluorescens [19,25] <9> Bacillus sp. (strain YM-1) [21] <10> Pseudomonas putida [24] <11> Penaeus monodon [26] <12> Tolypocladium niveum [27] <13> Serratia marcescens [29]

1 Alanine racemase 5.1.1.1

3 Reaction and Specificity

Catalyzed reaction l-Ala = d-Ala (<2>, the active site of the alanine racemase reacts asymme- trically with the enantiomers of the substrate and has a conformation which greatly favors the d-enantiomer [3]; <4>, the alanine racemase builds two different bases in the active site. The base for d-Ala may be closer to the enzyme surface, and that for l-Ala inside [18]) Reaction type Racemization Natural substrates l-Ala <3,4,7,9> (<3,4,9>, enzyme provides d-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall) [11,15,21,28] Additional information <3,12> (<3>, two nonhomologous alanine racemase genes, one of which is associated with the catabolic function and the other of which presumably represents the biosynthetic function [4]; <3>, alr racemase is constitutive and serves an anabolic function, dadB encoded enzyme is in- ducible and required for cell growth on l-Ala [14,24]; <12>, key enzyme in cyclosporin A biosynthesis [27]) [4,14,24,27] Substrates and products S L-Ala <1-13> (<1,4>, specific for Ala [1,8]) [1-31] P D-Ala <1-13> [1-31] S Additional information <2> (<2>, exchange of the a-hydrogen of d-Ala and l-Ala with D2O) [2] P ? Inhibitors (1-Aminoethyl)boronic acid <4> [16] (1-Aminoethyl)phosphonate <1,4> (<1>, d- and l-(1-aminoethyl)phosphonate [6]) [6,12] 2-Amino-3-chlorobut-3-enoic acid <7> (<7>, i.e. 3-chlorovinylglycine, irreversible [22]) [22,28] 2-Amino-3-fluorobut-3-enoic acid <7> (<7>, i.e. 3-fluorovinylglycine, irreversible [22]) [22,28] d-Chloroalanine <2,3> (<2>, Ki: 0.005 mM, competitive [3]) [3,7] d-O-Acetylserine <3> [7] d-b-Fluoroalanine <3> [7] FAD <11> (slight activation at low concentrations, inhibition at high concentrations) [26] l-Chloroalanine <2,3> (<2>, Ki: 1.71 mM, noncompetitive [3]) [3,7] l-b-Chloroalanine <3> [7] NaCl <11> (<11>, slight inhibition above 600 mM) [26] O-Carbamoyl-d-Ser <1> (<1>, inhibition of wild type enzyme but not of the O-carbamoyl-d-Ser mutant) [6]

2 5.1.1.1 Alanine racemase

Pyridoxal 5'-phosphate <11> (<11>, slight activation at low concentrations, inhibition at high concentrations) [26] Pyruvate <11> [26] Vinylglycine <5> [13] b,b,b-Trifluoroalanine <3,4> (<3,4>, nucleophilic attack of Lys38 on the elec- trophilic b-difluoro-a,b-unsaturated imine) [15] Cofactors / prostethic groups / activating substances FAD <11> (<11>, not required as cofactor, slight activation at low concentrations, inhibition at high concentrations) [26] Glutathione <1> (<1>, required for maximal activity) [1] Pyridoxal 5'-phosphate <1,3,4,8,12> (<1-4>, pyridoxal 5'-phosphate depen- dent enzyme [11,24]; <1,12>, required as coenzyme [1,27]; <3>, 1 mol of pyridoxal 5'-phosphate is bound per subunit [5]; <1>, 1 pyridoxal 5'-phosphate per 42000 MW subunit [6]; <3>, contains one mol of pyridoxal 5'- phosphate per mol of enzyme [7]; <3>, the sequence of 10 amino acid resi- dues around the Lys residue, to which pyridoxal 5'-phosphate is bound, is identical with that of the dadB racemase [7]; <3>, Km: 0.000033 mM [7]; <4, 8>, 2 mol of pyridoxal 5'-phosphate bound per mol of enzyme dimer [8,19]; <4>, the monomeric inactive enzyme appears to bind the cofactor pyridoxal 5'-phosphate by a non-covalent linkage, although the native dimeric enzyme binds the cofactor through an aldimine Schiff base linkage [17]; <1-4>, pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The a-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated [24]; <11>, not required as cofactor, slight activation at low concentrations, inhibition at high concentrations [26]; <4>, Arg219 forms a hydrogen bond with the pyridine nitrogen of the cofactor, Arg136 donates a hydrogen bond to the phenolic oxygen of pyridoxal 5'-phosphate and may be involved in the binding of substrate as well as stabilization of intermediates [30]) [1,5-8,11,17,19,24,26,27,30] Turnover number (min±1) 66 <4> (l-Ala, <4>) [11] 96 <3> (d-Ala, dadB encoded enzyme, <3>) [11] 156 <3> (d-Ala, alr encoded enzyme, <3>) [11] 420 <4> (d-Ala, <4>) [11] 438 <3> (l-Ala, dadB encoded enzyme, <3>) [11] 582 <3> (l-Ala, alr encoded enzyme, <3>) [11] Specific activity (U/mg) 22 <3> [7] 133 <7> [28] 143 <12> [27] 567 <11> [26] 587 <8> [19] 910 <3> [5] 2920 <1> [6] Additional information <1> [1]

3 Alanine racemase 5.1.1.1

Km-Value (mM) 0.5 <3> (d-Ala, alr gene encoded, <3>) [11] 1.7 <3> (l-Ala, alr gene encoded, <3>) [11] 2 <3,12> (d-Ala, <3,12>) [7,27] 2.1 <3> (d-Ala, <3>) [5] 2.2 <1,3> (d-Ala, <1> [6]; d-Ala, dadB encoded enzyme, <3> [11]) [6,11] 2.7 <3> (l-Ala, <3> [7]; d-Ala, <4> [8,11]) [7,8,11] 4.25 <4> (l-Ala, <4>) [8] 4.4 <4> (l-Ala, <4>) [11] 7.8 <1> (l-Ala, <1>) [6] 8.2 <3> (l-Ala, <3>) [5] 8.5 <1> (Ala, <1>) [1] 11 <3> (l-Ala, dadB gene encoded, <3>) [11] 12.8 <8> (d-Ala, <8>) [19] 18.9 <8> (l-Ala, <8>) [19] 119 <11> (d-Ala, <11>) [26] Additional information <4,8><4,8>, Km values of l-Ala in the presence of urea at various concentrations) [25] pH-Optimum 8.3 <8> [19] 8.5 <1,3,11> [1,7,26] 8.8 <12> (<12>, l-Ala) [27] 9 <1> [6] 9.5 <12> (<12>, d-Ala) [27] pH-Range 7±9.5 <11> (<11>, 7.0: about 45% of maximal activity, 9.5: about 95% of maximal activity) [26] Temperature optimum (C) 30 <8> [19] 35±40 <11> [26] 42 <12> (<12>, l-Ala) [27] Temperature range (C) 0±40 <8> (<8>, 0 C: about 25% of maximal activity, 40 C: about 45% of maximal activity) [19] 20±50 <11> (<11>, 20 C: about 60% of maximal activity, 50 C, about 35% of maximal activity) [26]

4 Enzyme Structure

Molecular weight 43000 <3> (<3>, gel filtration) [7] 50000 <3> (<3>, gel filtration) [5] 67000 <1> (<1>, gel filtration) [6]

4 5.1.1.1 Alanine racemase

76000 <8> (<8>, gel filtration in presence or absence of 2-mercaptoethanol) [19] 78000 <4> (<4>, equilibrium sedimentation method) [8] 85000 <11> (<11>, HPLC gel filtration) [26] 120000±150000 <12> (<12>, gel filtration) [27] Subunits ? <1,4,12> (<1>, x * 42000, SDS-PAGE [6]; <4>, x * 43341, calculation from nucleotide sequence [10,20]; <12>, 3 or 4 * 37000, SDS-PAGE [27]) [6,10,20, 27] Dimer <4,8> (<4>, 2 * 39000, SDS-PAGE [8]; <4> [14,24]; <8>, 2 * 38000, SDS-PAGE [19]) [8,14,19,24] Monomer <1,3> (<3>, 1 * 39000, SDS-PAGE [5]; <3>, 1 * 39044, calculation from nucleotide sequence [5]; <3>, 1 * 42000, SDS-PAGE [7]; <3> [14]; <3>, dadB enzyme and alr enzyme [24]; <1> [24]) [5,7,14,24]

5 Isolation/Preparation/Mutation/Application

Source/tissue Muscle <11> [26] Purification <1> [1,6] <3> (enzyme encoded by the dadB gene [5];alr gene encoded [7]) [5,7] <4> (enzyme overproduced in E. coli W3110 lacIq [9]) [8,9,20] <7> [28] <8> [19] <11> (partial) [26] <12> [27] Renaturation <4> (enzyme denatured in 6 M guanidine hydrochloride is renatured either by dialysis or dilution to reduce the guanidine hydrochloride concentration) [17] Crystallization <4> [9,30] Cloning <3> (two genes: dadA and dadB [4]; dadB [5]) [4,5] <4> (expression in E. coli C600 [8]; 31-54% sequence homologies with Bacil- lus subtilis and Salmonella typhimurium dadB and alr enzymes [10]; expression in E. coli [20,21]) [8,10,20,21] Engineering Additional information <3,4> (<3>, double mutant for the alr encoded enzyme and the dad B encoded enzyme display a phenotype of requirement for exogenous d-Ala for growth [14,24]; <4>, mutant gene which tandemly en- codes the two polypeptides of the enzyme subunit, fragment 1 and fragment

5 Alanine racemase 5.1.1.1

2, cleaved at the position corresponding to the predicted hinge region. The mutant fragmentary alanine racemase is active at about 40% of the activity of the wild type enzyme [21,23,24]) [14,21-24]

6 Stability pH-Stability 7.2 <3> (<3>, 80 C, stable) [24] 8.3±10.5 <4,8> (<4,8>, 1 h, 0 C, stable) [25] Temperature stability 20 <8> (<8>, 1 h, stable) [19] 30 <8> (<8>, over 30 C, 1 h, quick loss of activity [19,25]; <8>, 5 min, about 50% loss of activity after incubation with 0.08% SDS, 1 M guanidine hydrochloride, 4 M urea, 45% ethanol or 50% dimethyl sulfoxide [25]; <4>, 5 min, resistant to incubation with 0.08% SDS, 1 M guanidine hydrochloride, 4 M urea, 45% ethanol or 50% dimethyl sulfoxide [25]) [19,25] 40±50 <11> (<11>, pH 8.0, 5 min, sharp decrease of activity between 40 C and 50 C) [26] 60 <11> (<11>, pH 8.0, 5 min, almost complete inactivation) [26] 70 <3> (<3>, 80 min, pH 7.2, stable) [24] 75 <4> (<4>, 1 h, inactivation over 75 C) [25] General stability information <3>, NaB3H4-reduced DadB holoenzyme is resistant to a-chymotrypsin and trypsin and is labile only towards subtilisin [31] <3>, stable in 30% ammonium sulfate. Irreversibly diminished activity by exposure to ammonium sulfate concentrations near or above 40%, where pre- cipitation occurs [5] <4>, 5 min, resistant to incubation with 0.08% SDS, 1 M guanidine hydrochloride, 4 M urea, 45% ethanol or 50% dimethyl sulfoxide [25] <4>, denatured by 3.5 M urea in one transition phase [25] <4>, in 0.6 M to 1.5 M guanidine hydrochloride the dimeric enzyme is dis- sociated into a monomeric form, which is catalytically inactive [17,21] <8>, 5 min, about 50% loss of activity after incubation with 0.08% SDS, 1 M guanidine hydrochloride, 4 M urea, 45% ethanol or 50% dimethyl sulfoxide [25] <8>, denatured by urea in two transition phases, dissociation of pyridoxal 5'- phosphate with 4.0 M urea, unfolding with 5.5 M urea [25] Storage stability <3>, -70C, 10% glycerol, more than 90% of the activity is retained after 2 years [5] <8>, -20C, stable for 1 month [19] <8>, 4C, stable for 1 week [19] <11>, enzyme loses about 20% of activity during storage for 20 days at -20C, 0C and 5C [26]

6 5.1.1.1 Alanine racemase

References

[1] Wood, W.A.: Amino acid racemase. Methods Enzymol., 2, 212-217 (1955) [2] Babu, U.M.; Johnston, R.B.: D2O-alanine exchange reactions catalyzed by alanine racemase and glutamic pyruvic transaminase. Biochem. Biophys. Res. Commun., 58, 460-466 (1974) [3] Henderson, L.L.; Johnson, R.B.: Inhibition studies of the enantiomers of b- chloroalanine on purified alanine racemase from Bacillus subtilis. Biochem. Biophys. Res. Commun., 68, 793-798 (1976) [4] Wasserman, S.A.; Walsh, C.T.; Botstein, D.: Two alanine racemase genes in Salmonella typhimurium that differ in structure and function. J. Bacteriol., 153, 1439-1450 (1983) [5] Wasserman, S.A.; Daub, E.; Grisafi, P.; Botstein, D.; Walsh, C.T.: Catabolic alanine racemase from Salmonella typhimurium: DNA sequence, enzyme purification, and characterization. Biochemistry, 23, 5182-5187 (1984) [6] Badet, B.; Walsh, C.: Purification of an alanine racemase from Streptococ- cus faecalis and analysis of its inactivation by (1-aminoethyl)phosphonic acid enantiomers. Biochemistry, 24, 1333-1341 (1985) [7] Esaki, N.; Walsh, C.T.: Biosynthetic alanine racemase of Salmonella typhimurium: purification and characterization of the enzyme encoded by the alr gene. Biochemistry, 25, 3261-3267 (1986) [8] Inagaki, K.; Tanizawa, K.; Badet, B.; Walsh, C.T.; Tanaka, H.; Soda, K.: Ther- mostable alanine racemase from Bacillus stearothermophilus: molecular cloning of the gene, enzyme purification, and characterization. Biochemis- try, 25, 3268-3274 (1986) [9] Neidhart, D.J.; Distefano, M.D.; Tanizawa, K.; Soda, K.; Walsh, C.T.; Petsko, G.A.: X-ray crystallographic studies of the alanine-specific racemase from Bacillus stearothermophilus. J. Biol. Chem., 262, 15323-15326 (1987) [10] Tanizawa, K.; Ohshima, A.; Scheidegger, A.; Inagaki, K.; Tanaka, H.; Soda, K.: Thermostable alanine racemase from Bacillus stearothermophilus: DNA and protein sequence determination and secondary structure prediction. Biochemistry, 27, 1311-1316 (1988) [11] Faraci, W.S.; Walsh, C.T.: Racemization of alanine by the alanine racemase from Salmonella typhimurium and Bacillus stearothermophilus: energetic reaction profiles. Biochemistry, 27, 3267-3276 (1988) [12] Copie, V.; Faraci, W.S.; Walsh, C.T.; Griffin, R.G.: Inhibition of alanine racemase by alanine phosphonate: detection of an imine linkage to pyridoxal 5'-phosphate in the enzyme-inhibitor complex by solid-state 15N nuclear magnetic resonance. Biochemistry, 27, 4966-4970 (1988) [13] Lacoste, A.M.; Darriet, M.; Neuzil, E.; Le Goffic, F.: Inhibition of alanine racemase by vinylglycine and its phosphonic analogue: a 1H nuclear magnetic resonance spectroscopy study. Biochem. Soc. Trans., 16, 606-608 (1988) [14] Walsh, C.T.: Enzymes in the d-alanine branch of bacterial cell wall peptidoglycan assembly. J. Biol. Chem., 264, 2393-2396 (1989)

7 Alanine racemase 5.1.1.1

[15] Faraci, W.S.; Walsh, C.T.: Mechanism of inactivation of alanine racemase by b,b,b-trifluoroalanine. Biochemistry, 28, 431-437 (1989) [16] Duncan, K.; Faraci, W.S.; Matteson, D.S.; Walsh, C.T.: (1-Aminoethyl)boronic acid: a novel inhibitor for Bacillus stearothermophilus alanine racemase and Salmonella typhimurium d-alanine:D-alanine ligase (ADP-forming). Biochemistry, 28, 3541-3549 (1989) [17] Toyama, H.; Esaki, N.; Yoshimura, T.; Tanizawa, K.; Soda, K.: Thermostable alanine racemase of Bacillus stearothermophilus: subunit dissociation and unfolding. J. Biochem., 110, 279-283 (1991) [18] Sawada, S.; Tanaka, Y.; Hayashi,S.; Ryu, M.; Hasegawa, T.; Yamamoto, Y.; Esaki, N.; Soda, K.; Takahashi, S.: Kinetics of thermostable alanine racemase of Bacillus stearothermophilus. Biosci. Biotechnol. Biochem., 58, 807-811 (1994) [19] Yokoigawa, K.; Kawai, H.; Endo, K.; Lim, Y.H.; Esaki, N.; Soda, K.: Thermo- labile alanine racemase from a psychrotroph, Pseudomonas fluorescens: purification and properties. Biosci. Biotechnol. Biochem., 57, 93-97 (1993) [20] Soda, K.; Tanizawa, K.: Thermostable alanine racemase. Its structural stability. Ann. N. Y. Acad. Sci., 585, 386-393 (1990) [21] Soda, K.; Esaki, N.: Pyridoxal enzymes acting on d-amino acids. Pure Appl. Chem., 66, 709-714 (1994) [22] Thornberry, N.A.; Bull, H.G.; Taub, D.; Greenlee, W.J.; Patchett, A.A.; Cordes, E.H.: Halovinylglycines. Efficient irreversible inhibitors of E. coli alanine racemase. J. Am. Chem. Soc., 109, 7543-7544 (1987) [23] Toyama, H.; Tanizawa, K.; Wakayama, M.; Lee, Q.-L.; Yoshimura, T.; Esaki, N.; Soda, K.: Limited proteolysis of thermostable alanine racemase of Bacil- lus stearothermophilus. Agric. Biol. Chem., 55, 2881-2882 (1991) [24] Yoshimura, T.; Esaki, N.; Soda, K.: Structure and function of alanine racemase. Bull. Inst. Chem. Res., 70, 378-384 (1992) [25] Okubo, Y.; Tomioka, R.; Yokoigawa, K.; Kawai, H.: Lability of alanine racemase from a psychrotroph. J. Home Econ. Jpn., 46, 1135-1140 (1995) [26] Fujita, E.; Okuma, E.; Abe, H.: Partial purification and properties of alanine racemase from the muscle of black tiger prawn Penaeus monodon. Fish- eries Sci., 63, 440-445 (1997) [27] Hoffmann, K.; Schneider-Scherzer, E.; Kleinkauf, H.; Zocher, R.: Purifica- tion and characterization of eucaryotic alanine racemase acting as key enzyme in cyclosporin biosynthesis. J. Biol. Chem., 269, 12710-12714 (1994) [28] Thornberry, N.A.; Bull, H.G.; Taub, D.; Wilson, K.E.; Gimenez-Gallego, G.; Rosegay, A.; Soderman, D.D.; Patchett, A.A.: Mechanism-based inactivation of alanine racemase by 3-halovinylglycines. J. Biol. Chem., 266, 21657-21665 (1991) [29] Zboinska, E.; Sztajer, H.; Lejczak, B.; Kafarski, P.: Antibacterial activity of phosphono dipeptides based on 1-amino-1-methylethanephosphonic acid. FEMS Microbiol. Lett., 58, 23-28 (1990) [30] Shaw, J.P.; Petsko, G.A.; Ringe, D.: Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution. Biochemis- try, 36, 1329-1342 (1997)

8 5.1.1.1 Alanine racemase

[31] Galaktos, N.G.; Walsh, C.T.: Specific proteolysis of native alanine racemases from Salmonella typhimurium: identification of the cleavage site and characterization of the clipped two-domain proteins. Biochemistry, 26, 8475- 8480 (1987)

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