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Crystals, volume 12, issue 5, pages 619

A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine

Nikolaeva Alena Y. 1, 2
Rakitina Tatiana V. 1, 3
Popov Vladimir O. 1, 2
Bezsudnova Ekaterina Yu 1
Publication typeJournal Article
Publication date2022-04-26
Journal: Crystals
Quartile SCImago
Q2
Quartile WOS
Q2
Impact factor2.7
ISSN20734352, 01725076
Inorganic Chemistry
General Chemical Engineering
Condensed Matter Physics
General Materials Science
Abstract

Effective biocatalysts for the synthesis of optically pure amines from keto precursors are highly required in organic synthesis. Transaminases are a large group of PLP-dependent enzymes, which can be utilized for production of chiral amines or amino acids. The bioinformatic approach previously made to search for promising transaminases with unusual characteristics surprisingly revealed mysterious genes in some Gram-negative bacteria, which products were annotated as aminotransferases, but they lacked the key catalytic lysine residue required for covalent binding of the PLP-cofactor. To address the question of which products these genes encode, we obtained the first structure of such a type of protein from the bacterium Variovorax paradoxus (VP5454) and provided its comprehensive analysis. We demonstrated that VP5454 has a typical aminotransferase fold and architecture of the active site, where substitution of the catalytic lysine with asparagine was observed. Despite that no covalent adduct can be formed between PLP and asparagine residue, using X-ray analysis and molecular dynamic (MD) simulation, we demonstrated that VP5454 is able to bind the PLP molecule in the transaminase in a specific manner, with PLP coordinated via its phosphate moiety. Taking into account a number of sequences homologous to VP5454 with a substituted catalytic lysine found in the genomes of various bacteria, we speculate that the proteins encoded by these sequences may have hidden functional roles.

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Boyko K. M. et al. A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine // Crystals. 2022. Vol. 12. No. 5. p. 619.
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Boyko K. M., Matyuta I. O., Nikolaeva A. Y., Rakitina T. V., Popov V. O., Bezsudnova E. Yu., Khrenova M. G. A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine // Crystals. 2022. Vol. 12. No. 5. p. 619.
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TY - JOUR
DO - 10.3390/cryst12050619
UR - https://doi.org/10.3390%2Fcryst12050619
TI - A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine
T2 - Crystals
AU - Nikolaeva, Alena Y.
AU - Rakitina, Tatiana V.
AU - Popov, Vladimir O.
AU - Bezsudnova, Ekaterina Yu
AU - Boyko, Konstantin M.
AU - Matyuta, Ilya O.
AU - Khrenova, Maria G.
PY - 2022
DA - 2022/04/26 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 619
IS - 5
VL - 12
SN - 2073-4352
SN - 0172-5076
ER -
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@article{2022_Boyko
author = {Alena Y. Nikolaeva and Tatiana V. Rakitina and Vladimir O. Popov and Ekaterina Yu Bezsudnova and Konstantin M. Boyko and Ilya O. Matyuta and Maria G. Khrenova},
title = {A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine},
journal = {Crystals},
year = {2022},
volume = {12},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {apr},
url = {https://doi.org/10.3390%2Fcryst12050619},
number = {5},
pages = {619},
doi = {10.3390/cryst12050619}
}
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Boyko, Konstantin M., et al. “A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine.” Crystals, vol. 12, no. 5, Apr. 2022, p. 619. https://doi.org/10.3390%2Fcryst12050619.
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