To the Understanding of Catalysis by D-Amino Acid Transaminases : A Case Study of the Enzyme from Aminobacterium colombiense
Pyridoxal-5'-phosphate (PLP)-dependent transaminases are highly efficient biocatalysts for stereoselective amination. D-amino acid transaminases can catalyze stereoselective transamination producing optically pure D-amino acids. The knowledge of substrate binding mode and substrate differentiation mechanism in D-amino acid transaminases comes down to the analysis of the transaminase from Bacillus subtilis. However, at least two groups of D-amino acid transaminases differing in the active site organization are known today. Here, we present a detailed study of D-amino acid transaminase from the gram-negative bacterium Aminobacterium colombiense with a substrate binding mode different from that for the transaminase from B. subtilis. We study the enzyme using kinetic analysis, molecular modeling, and structural analysis of holoenzyme and its complex with D-glutamate. We compare the multipoint binding of D-glutamate with the binding of other substrates, D-aspartate and D-ornithine. QM/MM MD simulation reveals that the substrate can act as a base and its proton can be transferred from the amino group to the α-carboxylate group. This process occurs simultaneously with the nucleophilic attack of the PLP carbon atom by the nitrogen atom of the substrate forming gem-diamine at the transimination step. This explains the absence of the catalytic activity toward (R)-amines that lack an α-carboxylate group. The obtained results clarify another substrate binding mode in D-amino acid transaminases and underpinned the substrate activation mechanism.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:28 |
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| Enthalten in: |
Molecules (Basel, Switzerland) - 28(2023), 5 vom: 23. Feb. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Shilova, Sofia A [VerfasserIn] |
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| Links: |
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| Themen: |
3KX376GY7L |
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| Anmerkungen: |
Date Completed 14.03.2023 Date Revised 14.03.2023 published: Electronic Citation Status MEDLINE |
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| doi: |
10.3390/molecules28052109 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM354089900 |
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| 100 | 1 | |a Shilova, Sofia A |e verfasserin |4 aut | |
| 245 | 1 | 3 | |a To the Understanding of Catalysis by D-Amino Acid Transaminases |b A Case Study of the Enzyme from Aminobacterium colombiense |
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| 500 | |a Date Revised 14.03.2023 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Pyridoxal-5'-phosphate (PLP)-dependent transaminases are highly efficient biocatalysts for stereoselective amination. D-amino acid transaminases can catalyze stereoselective transamination producing optically pure D-amino acids. The knowledge of substrate binding mode and substrate differentiation mechanism in D-amino acid transaminases comes down to the analysis of the transaminase from Bacillus subtilis. However, at least two groups of D-amino acid transaminases differing in the active site organization are known today. Here, we present a detailed study of D-amino acid transaminase from the gram-negative bacterium Aminobacterium colombiense with a substrate binding mode different from that for the transaminase from B. subtilis. We study the enzyme using kinetic analysis, molecular modeling, and structural analysis of holoenzyme and its complex with D-glutamate. We compare the multipoint binding of D-glutamate with the binding of other substrates, D-aspartate and D-ornithine. QM/MM MD simulation reveals that the substrate can act as a base and its proton can be transferred from the amino group to the α-carboxylate group. This process occurs simultaneously with the nucleophilic attack of the PLP carbon atom by the nitrogen atom of the substrate forming gem-diamine at the transimination step. This explains the absence of the catalytic activity toward (R)-amines that lack an α-carboxylate group. The obtained results clarify another substrate binding mode in D-amino acid transaminases and underpinned the substrate activation mechanism | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a D-amino acids | |
| 650 | 4 | |a X-ray analysis | |
| 650 | 4 | |a enzymes | |
| 650 | 4 | |a structure | |
| 650 | 4 | |a substrate-assisted catalysis | |
| 650 | 4 | |a transaminase | |
| 650 | 7 | |a Amino Acids |2 NLM | |
| 650 | 7 | |a Transaminases |2 NLM | |
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| 650 | 7 | |a Glutamic Acid |2 NLM | |
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| 700 | 1 | |a Khrenova, Maria G |e verfasserin |4 aut | |
| 700 | 1 | |a Matyuta, Ilya O |e verfasserin |4 aut | |
| 700 | 1 | |a Nikolaeva, Alena Y |e verfasserin |4 aut | |
| 700 | 1 | |a Rakitina, Tatiana V |e verfasserin |4 aut | |
| 700 | 1 | |a Klyachko, Natalia L |e verfasserin |4 aut | |
| 700 | 1 | |a Minyaev, Mikhail E |e verfasserin |4 aut | |
| 700 | 1 | |a Boyko, Konstantin M |e verfasserin |4 aut | |
| 700 | 1 | |a Popov, Vladimir O |e verfasserin |4 aut | |
| 700 | 1 | |a Bezsudnova, Ekaterina Yu |e verfasserin |4 aut | |
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| 856 | 4 | 0 | |u http://dx.doi.org/10.3390/molecules28052109 |3 Volltext |
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