Structure prediction and evolution of a halo-acid dehalogenase of Burkholderia mallei

Environmental pollutants containing halogenated organic compounds e.g. haloacid, can cause a plethora of health problems. Thestructural and functional analyses of the gene responsible of their degradation are an important aspect for environmental studiesand are important to human well-being. It has been shown that some haloacids are toxic and mutagenic. Microorganisms capableof degrading these haloacids can be found in the natural environment. One of these, a soil-borne Burkholderia mallei posses theability to grow on monobromoacetate (MBA). This bacterium produces a haloacid dehalogenase that allows the cell to grow onMBA, a highly toxic and mutagenic environmental pollutant. For the structural and functional analysis, a 346 amino acid encodingprotein sequence of haloacid dehalogenase is retrieve from NCBI data base. Primary and secondary structure analysis suggestedthat the high percentage of helices in the structure makes the protein more flexible for folding, which might increase proteininteractions. The consensus protein sub-cellular localization predictions suggest that dehalogenase protein is a periplasmic protein3D2GO server, suggesting that it is mainly employed in metabolic process followed by hydrolase activity and catalytic activity. Thetertiary structure of protein was predicted by homology modeling. The result suggests that the protein is an unstable protein whichis also an important characteristic of active enzyme enabling them to bind various cofactors and substrate for proper functioning.Validation of 3D structure was done using Ramachandran plot ProsA-web and RMSD score. This predicted information will helpin better understanding of mechanism underlying haloacid dehalogenase encoding protein and its evolutionary relationship.