Homology Modeling of Bifunctional Enzyme Alanine Racemase from Taibaiella Chishuiensis

Abstract

ABSTRACT: Alanine Racemase from Taibaiella chishuiensis bacteria is one of the bifunctional enzymes that catalyze the L- and D-alanine racemization of peptidoglycan biosynthesis in bacteria and ligation (UDP-N-acetylmuramoyl-Tripeptide-D-alanyl-D-alanine ligase). It had two EC numbers 5.1.1.1 and 6.3.2.10 respectively. This enzyme is an important target for antimicrobial drug productions or inhibitor design. However, the 3D structure of Alanine Racemase from Taibaiella or UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase/alanine racemase has remained unknown. Thus, this study modeled and validated the 3D structure of the enzyme in the query. The bioinformatics tools/databases and software such as BRENDA, NCBI, UniProt, Clustal Omega, ProtParam, Swiss model, Phyre2, GOR, PROCHECK, and PyMOL were used for modeling, validation, and structural comparison. From the sequence and 3D structure analysis, it is indicated that Alanine racemase from Taibaiella had the same active and binding sites with the reference enzymes. Thus, we were able to study the similarities and differences in the sequence and structural properties of alanine racemase in two different bacteria. Finally, it was found that our enzyme has two parts for two different functions (racemization and ligation). The predicted model of alanine racemase of T. chishuiensis from this study could serve as a useful model for further study regarding the other bifunctional enzymes structure and function as well as drug design projects.