To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense

To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense Full article

Journal

Molecules
ISSN: 1420-3049

Output data

Year: 2023, Volume: 28, Number: 5, Article number : 2109, Pages count : DOI: 10.3390/molecules28052109

Authors

Shilova Sofia A. ¹ , Khrenova Maria G. ^1,2 , Matyuta Ilya O. ¹ , Nikolaeva Alena Y. ^1,3 , Rakitina Tatiana V. ^1,4 , Klyachko Natalia L. ² , Minyaev Mikhail E. ⁵ , Boyko Konstantin M. ¹ , Popov Vladimir O. ^1,6 , Bezsudnova Ekaterina Yu. ¹

Affiliations

1	Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
2	Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
3	Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
4	Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
5	N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
6	Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia

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.

Shilova S.A. , Khrenova M.G. , Matyuta I.O. , Nikolaeva A.Y. , Rakitina T.V. , Klyachko N.L. , Minyaev M.E. , Boyko K.M. , Popov V.O. , Bezsudnova E.Y.
To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense
Molecules. 2023. V.28. N5. 2109 . DOI: 10.3390/molecules28052109 WOS Scopus OpenAlex

≡ Web of science:	WOS:000948236200001
≡ Scopus:	2-s2.0-85149811145
≡ OpenAlex:	W4321789393