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Bioinformatic Analysis of Substrate Binding Sites in Decapod Brachyurin-C Collagenases

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Abstract

Brachyurin-C is the only member of the chymotrypsin A family able to hydrolyze native collagen type I and it is found in decapods like crabs, shrimps, lobsters, prawns, and crayfishes. Contrary to other members of the chymotrypsin family, two different types of specificity had been found in brachyurin-C, one that includes trypsin, chymotrypsin, and elastase combined and another with a preference to hydrophobic and small residues. In this work, through a bioinformatics approach the brachyurin family was analyzed. Brachyurin can be expressed as isoforms in some decapods with seven triplet residues combinations that formed the prime substrate binding or specific pocket at positions 189, 216 and 226 (GGD/GVD/SGA/SGD/GGA/GAE/GSD). By protein modeling a third specificity kind is predicted in which preference could be greater to small residues due steric impediment. The obstruction at the prime substrate binding depends on the substitution of ramified residues side chains at one of the walls of site 216 in which Val/Ser could reduce the entrance to the specific pocket. Eight specific-determinant positions were obtained with two potential substrate subsites on two loops (93–96, 98, 100 and 177, 179) that differ from the chymotrypsin A subfamily loops involved in the substrate distal binding. The residue replacement at specific-determinant positions in brachyurins formed two different subsets that do not followed specificity preference. Phylogenetic analysis does not reflect substrate preference, though the results on specific-determinant positions and the phylogenetic of brachyurins showed that the former classification based only in their substrate preference should be reconsidered.

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ACKNOWLEDGMENTS

The author thanks Crisalejandra Rivera-Perez for her experienced suggestions, Claudia Maytorena-Verdugo for editing the manuscript and Julio Hernández-Gonzalez for his help with the bioinformatics search. The author appreciates the observations and recommendations of the anonymous reviewers.

Funding

The study was supported by CIBNOR grant no. PP 10023.

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  1. Centro de Investigaciones Biologicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195 La Paz, B.C.S. 23096, Mexico, Mexico

    P. Hernandez-Cortes

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Correspondence to P. Hernandez-Cortes.

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This study did not involve human subjects as research objects.

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The author declares that she has no conflict of interest.

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The original online version of this article was revised: the issue date is not January 2020, but January 2021

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Hernandez-Cortes, P. Bioinformatic Analysis of Substrate Binding Sites in Decapod Brachyurin-C Collagenases. J Evol Biochem Phys 57, 115–125 (2021). https://doi.org/10.1134/S0022093021010117

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