Yasuhiro Ikenaka

Crystal structure of N-carbamyl-d-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases

BACKGROUND N-carbamyl-D-amino acid amidohydrolase (DCase) catalyzes the hydrolysis of N-carbamyl-D-amino acids to the corresponding D-amino acids, which are useful intermediates in the preparation of beta-lactam antibiotics. To understand the catalytic mechanism of N-carbamyl-D-amino acid hydrolysis, the substrate specificity and thermostability of the enzyme, we have determined the structure of DCase from Agrobacterium sp. strain KNK712. RESULTS The crystal structure of DCase has been determined to 1.7 A resolution. The enzyme forms a homotetramer and each monomer consists of a variant of the alpha + beta fold. The topology of the enzyme comprises a sandwich of parallel beta sheets surrounded by two layers of alpha helices, this topology has not been observed in other amidohydrolases such as the N-terminal nucleophile (Ntn) hydrolases. CONCLUSIONS The catalytic center could be identified and consists of Glu46, Lys126 and Cys171. Cys171 was found to be the catalytic nucleophile, and its nucleophilic character appeared to be increased through general-base activation by Glu46. DCase shows only weak sequence similarity with a family of amidohydrolases, including beta-alanine synthase, aliphatic amidases and nitrilases, but might share highly conserved residues in a novel framework, which could provide a possible explanation for the catalytic mechanism for this family of enzymes.

Microbial synthesis of (R)- and (S)-3,4-dimethoxyamphetamines through stereoselective transamination

Two soil isolates, Arthrobacter sp. KNK168 and Pseudomonas sp. KNK425, aminated 3,4-dimethoxyphenylacetone in presence of sec-butylamine as an amino donor to yield 3,4-dimethoxyamphetamine (DMA) with different enantioselectivities. The former gave (R)-DMA (>99% e.e.) and the latter the (S)-isomer (>99% e.e.).

Production of thermotolerant N-carbamyl-D-amino acid amidohydrolase by recombinant Escherichia coli

A plasmid, pNT4553, was constructed for high level production of N-carbamyl-d-amino acid amidohydrolase (DCase), the thermostability of which has been improved by amino acid substitution. The DCase activity and the stability of the plasmid in the host cells were dependent on the Escherichia coli strains used. E. coli HB101 was the most suitable host strain among the 13 types of E. coli tested. E. coli HB101 exhibited the highest activity, i.e. 6.36 units/ml of culture broth in 2YT medium (1.6% tryptone, 1.0% yeast extract, and 0.5% NaCl, pH 7.0), and the plasmid was stably maintained by cultivation in 5 types of E. coli including HB101. Casamino acids, NZ-amine, peptone, and protein extract (a mixture of hydrolyzates of corn gluten, wheat gluten and soybean), were found to be suitable as natural nitrogen sources for both enzyme activity and growth. When cultivation was carried out in the presence of high concentrations of glycerol (6.5%) as the carbon source, and protein extract (3.0%) as the nitrogen source, in a small volume of the medium (20 ml of medium in a 500-ml shaking flask), in which the aeration level was estimated to be high, growth and activity reached OD550=63.8 (17.1 mg of dry cell weight/ml of culture broth) and 22.9 units/ml of culture broth, respectively. The economical hyperproduction of DCase using only inexpensive constituents for the medium was achieved.

Immobilization of thermotolerant N-carbamyl-D-amino acid amidohydrolase.

Abstract N-Carbamyl- d -amino acid amidohydrolase (DCase), in which amino acid residues were substituted by mutation, followed by the selection based on thermotolerance, showed improved thermostability, by 5° or 10°C, compared to the native DCase. These DCases were immobilized on a macroporous phenol formaldehyde resin, Duolite A-568, and the immobilized thermotolerant enzymes showed higher activity than the immobilized native DCase. From the results of repeated batch reactions, the half-lives of the activities of immobilized thermotolerant DCase, in which Leu was substituted for Pro 203, and immobilized native DCase were 104 and 58 times, respectively. It was revealed that the higher thermotolerance enabled the immobilized enzymes to be more stable in reactions. A reductant, dithiothreitol, also stabilized the enzymes in reactions. Compared with soluble DCase, immobilized DCase was somewhat stable, and its activity was optimum at a lower pH.

β-Carbon stereoselectivity of N-carbamoyl-d-α-amino acid amidohydrolase for α,β-diastereomeric amino acids

N-Carbamoyl-d-α-amino acid amidohydrolase (d-carbamoylase) was found to distinguish stereochemistry not only at the α-carbon but also at the β-carbon of N-carbamoyl-d-α-amino acids. The enzyme selectively acted on one of the four stereoisomers of N-carbamoyl-α,β-diastereomeric amino acids. This simultaneous recognition of two chiral centers by d-carbamoylase was useful for the fine stereoselective synthesis of α,β-diastereomeric amino acids such as threonine, isoleucine, 3,4-methylenedioxyphenylserine and β-methylphenylalanine. The stereoselectivity for the β-carbon was influenced by the pH of the reaction mixture and by the bulk of the substituent at the β-carbon.

Cloning and characterization of decaprenyl diphosphate synthase from three different fungi

Coenzyme Q (CoQ) is composed of a benzoquinone moiety and an isoprenoid side chain of varying lengths. The length of the side chain is controlled by polyprenyl diphosphate synthase. In this study, dps1 genes encoding decaprenyl diphosphate synthase were cloned from three fungi: Bulleromyces albus, Saitoella complicata, and Rhodotorula minuta. The predicted Dps1 proteins contained seven conserved domains found in typical polyprenyl diphosphate synthases and were 528, 440, and 537 amino acids in length in B. albus, S. complicata, and R. minuta, respectively. Escherichia coli expressing the fungal dps1 genes produced CoQ10 in addition to endogenous CoQ8. Two of the three fungal dps1 genes (from S. complicata and R. minuta) were able to replace the function of ispB in an E. coli mutant strain. In vitro enzymatic activities were also detected in recombinant strains. The three dps1 genes were able to complement a Schizosaccharomyces pombedps1, dlp1 double mutant. Recombinant S. pombe produced mainly CoQ10, indicating that the introduced genes were independently functional and did not require dlp1. The cloning of dps1 genes from various fungi has the potential to enhance production of CoQ10 in other organisms.

Aminohydrolases, for Production of D-Amino Acids

Introduction Screening of N-Carbamoyl-d-Amino Acid Amidohydrolase Screening of DCase-Producing Microorganisms Purification and Characterization of the Enzymes Isolation of Enzyme Genes Cloning of Enzyme Genes Analysis of the Enzyme Genes Improvement of the Enzyme in Stability Mutagenesis Nucleotide Sequence Analysis of the Mutagenized DCase Genes Amino Acid Substitution of Thermostability-Related Sites by PCR Combination of Thermostability-Related Mutations Characterization of the Thermostabilized Enzymes Effects of Temperature and pH on Enzyme Stability Substrate Specificities of the DCases Kinetic Properties of the Enzymes Production of an Improved Enzyme Construction of an Expression Vector Expression of the Thermostabilized Enzyme Preparation of an Immobilized Enzyme Immobilization of the Improved DCase Stability of the Immobilized Enzyme Utilization of the Improved DCase for Industrial Production Bibliography Keywords: d-amino acid; N-carbamoyl-d-amino acid amidohydrolase; thermotolerant enzyme