Characterization of hydantoin racemase predicted from the genome sequence ofLactobacillus pentosusKCA1

Abstract

Background: Hydantoin racemase from Lactobacillus species of human origin has not been reported and characterized. The genome of Lactobacillus pentosus KCA1 has been sequenced and found to possess gene cassettes and open reading frames encoding the hydantoinase machinery, including a putative hydantoin racemase. Aims: To use bioinformatic tools to characterize the new hydantoin racemase predicted in the genome sequence of L. pentosus KCA1. Materials and Methods: Bioinformatic tools such as ClustalW algorithm was used to align hydantoin racemase from L. pentosus KCA1 with other hydantoin racemases extracted from the uniprot΢ database. I-TASSER was used for the prediction of secondary structure, 3-D model, similarity structure in PDB, and functional active binding site residues. Results: L. pentosus KCA1 hydantoin racemase showed significant amino acid sequence identity with hydantoin racemase from the selected bacterial organisms in the protein databank (PDB). The predicted secondary structure revealed 9 alpha-helices and 8 beta-strands. Functional prediction using enzyme partners predicted EC number 5.1.1.13 as the corresponding enzyme homolog (3eq5A) showing Cys83 and Cys187 as the potential active residues in KCA1 hydantoin racemase. The 3-D structure of KCA1 hydantoin racemase has a confidence score (C-score) of 1.2 that reflects a model of better quality, based on 3qvjA from PDB. Conclusion: The in silico data presented provides new insights into the potential activity and substrate specificity of hydantoin racemase from L. pentosus KCA1 and has proposed a mechanism for racemization of hydantoin derivatives that is consistent with the two-base process observed in other members of the Aspartate/Glutamate superfamily.