D-amino acid oxidase: structure, catalytic mechanism, and practical application

Тишков, В. И.; Khoronenkova, Svetlana V.

doi:10.1007/pl00021754

Cited by 16 publications

(10 citation statements)

References 115 publications

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“…The presence of arginine and tyrosine residues (R285 and Y223 in RtoDAAO and R302 and Y243 in TvaDAAO) in the active site was considered mandatory for binding the carboxyl group of the D-amino acid. Similar residues are also present in mammalian enzymes [ 1 , 2 ]. However, the expansion of the set of compared sequences indicates that only the fingerprint sequence in the FAD-binding domain and the arginine residue participating in binding the carboxyl group remain conserved.…”

Section: Resultsmentioning

confidence: 86%

“…Four DAAOs and DASPO were obtained in a highly purified form, their catalytic parameters with D-amino acids were determined, their activity and stability dependencies were studied at different medium pH values, and their thermal stability at pH values optimal for stability was studied. The amino acid sequences of vertebrate DAAO were not used because they initially had low homology with microbial enzymes [ 1 , 2 , 9 ].…”

Section: Resultsmentioning

confidence: 99%

“…A good example is D-amino acid oxidase (DAAO, EC 1.4.3.3). In bacteria, yeast, and fungi, the main role of this enzyme is limited to the utilization of exogenous D-amino acids (primarily D-Ala) [ 1 , 2 ]. In higher eukaryotes – vertebrates and especially in mammals, the main role of DAAO is to maintain a certain level of D-amino acids, which are regulators of many important processes, primarily nervous activity.…”

Section: Introductionmentioning

confidence: 99%

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Bioinformatics-Structural Approach to the Search for New D-Amino Acid Oxidases

et al. 2023

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D-amino acid oxidase (DAAO, EC 1.2.1.2) plays an important role in the functioning of prokaryotes as well as of lower (yeast and fungi) and higher eukaryotes (mammals). DAAO genes have not yet been found in archaean genomes. D-amino acid oxidase is increasingly used in various fields, which requires the development of new variants of the enzyme with specific properties. However, even within one related group (bacteria, yeasts and fungi, mammals), DAAOs show very low homology between amino acid sequences. In particular, this fact is clearly observed in the case of DAAO from bacteria. The high variability in the primary structures of DAAO severely limits the search for new enzymes in known genomes. As a result, many (if not most) DAAO genes remain either unannotated or incorrectly annotated. We propose an approach that uses bioinformatic methods in combination with general 3D structure and active center structure analysis to confirm that the gene found encodes D-amino acid oxidase and to predict the possible type of its substrate specificity. Using a homology search, we obtained a set of candidate sequences, modelled the tertiary structure of the selected enzymes, and compared them with experimental and model structures of known DAAOs. The effectiveness of the proposed approach for discrimination of DAAOs and glycine oxidases is shown. Using this approach, new DAAO genes were found in the genomes of six strains of extremophilic bacteria, and for the first time in the world, one gene was identified in the genome of halophilic archaea. Preliminary experiments confirmed the predicted specificity of DAAO from Natronosporangium hydrolyticum ACPA39 with D-Leu and D-Phe.

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Section: Resultsmentioning

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Bioinformatics-Structural Approach to the Search for New D-Amino Acid Oxidases

et al. 2023

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“…This property has made DAAO an effective tool for identifying and quantifying D ‐AAs in food production (Rosini et al, 2008). However, natural DAAOs have extremely low catalytic activity toward acidic AAs and a narrow acceptance range for nonnatural substrates (Sacchi et al, 2002; Tishkov & Khoronenkova, 2005). One well‐known example is the enantiomer D ‐phosphinothricin ( D ‐PPT) of the herbicide L ‐PPT (a glutamate analog) (Dayan, 2019).…”

Section: Introductionmentioning

confidence: 99%

Enhancement of the substrate specificity of D‐amino acid oxidase based on tunnel‐pocket engineering

Wang,

Tang,

Zhu

et al. 2023

Biotech & Bioengineering

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D‐Amino acid oxidase (DAAO) selectively catalyzes the oxidative deamination of D‐amino acids, making it one of the most promising routes for synthesizing optically pure L‐amino acids, including L‐phosphinothricin ( L‐PPT), a chiral herbicide with significant market potential. However, the native DAAOs that have been reported have low activity against unnatural acid substrate D‐PPT. Herein, we designed and screened a DAAO from Rhodotorula taiwanensis (RtwDAAO), and improved its catalytic potential toward D‐PPT through protein engineering. A semirational design approach was employed to create a mutation library based on the tunnel‐pocket engineering. After three rounds of iterative saturation mutagenesis, the optimal variant M3rd‐SHVG was obtained, exhibiting a >2000‐fold increase in relative activity. The kinetic parameters showed that M3rd‐SHVG improved the substrate binding affinity and turnover number. This is the optimal parameter reported so far. Further, molecular dynamics simulation revealed that the M3rd‐SHVG reshapes the tunnel‐pocket and corrects the direction of enzyme–substrate binding, allowing efficiently catalyze unnatural substrates. Our strategy demonstrates that the redesign of tunnel‐pockets is effective in improving the activity and kinetic efficiency of DAAO, which provides a valuable reference for enzymatic catalysis. With the M3rd‐SHVG as biocatalyst, 500 mM D, L‐PPT was completely converted and the yield reached 98%. The results laid the foundation for further industrial production.

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“…d -Amino acid oxidase (DAAO; EC:1.4.3.3) catalyzes the oxidation of d -amino acids to produce the corresponding α-keto acids, leading to the disassembly of chiral amino acids and the generation of key intermediates. , DAAO plays a crucial role in the synthesis of drugs, pesticides, and fine chemicals due to its broad substrate spectrum and high enantioselectivity. − In our previous study, Rtw DAAO from Rhodotorula taiwanensis was cloned and expressed. Following modification, the variant SHVG has been demonstrated to exhibit higher kinetic parameters toward the non-natural substrate d -phosphinothricin ( D -PPT) .…”

Section: Introductionmentioning

confidence: 99%

Correlation Analysis of Key Residue Sites between Computational-Aided Design Thermostability d-Amino Acid Oxidase and Ancestral Enzymes

Wang,

Tang,

Zhao

et al. 2023

J. Agric. Food Chem.

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D-amino acid oxidase: structure, catalytic mechanism, and practical application

Cited by 16 publications

References 115 publications

Bioinformatics-Structural Approach to the Search for New D-Amino Acid Oxidases

Bioinformatics-Structural Approach to the Search for New D-Amino Acid Oxidases

Enhancement of the substrate specificity of D‐amino acid oxidase based on tunnel‐pocket engineering

Correlation Analysis of Key Residue Sites between Computational-Aided Design Thermostability d-Amino Acid Oxidase and Ancestral Enzymes

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