Analysis of Haloacid Dehalogenase superfamily members and functional assignment of structural genomics proteins

Abstract

Dehalogenases are enzymes that can degrade certain types of organic pollutants, particularly halogenated hydrocarbons, into non-toxic compounds. In this research, the members of the haloacid dehalogenase (HAD) superfamily are analyzed to predict their biochemical function, with the ultimate goal of finding enzymes for possible application to the bioremediation of environmental contaminants. The HAD superfamily consists of mainly phosphatases, dehalogenases, and a large number of protein structures of unknown or uncertain function from Structural Genomics (SG). To study the HAD superfamily, the computational methods Partial Order Optimum Likelihood (POOL) and Structurally Aligned Local Sites of Activity (SALSA) are utilized. From this study, the SG protein RSc1362 from Ralstonia solanacearum (PDB ID 3UMB) is predicted to function as an L-2 haloacid dehalogenase while HAD/COF-like hydrolase from Plasmodium vivax (PDB ID 2B30), a hypothetical protein from Geobacillus kaustophilus (PDB ID 2PQ0), putative phosphate from Eubacterium Rectale (PDB ID 3DAO), and haloacid dehalogenase-like hydrolase from Bacteroides thetaiotaomicron (PDB ID 3NIW) are predicted to function as sugar phosphatases.