Knowledge-based modeling of a bacterial dichloromethane dehalogenase.
A three-dimensional structural model of the dichloromethane dehalogenase (DCMD) from Methylophilus sp. DM11 is constructed based on sequence similarities to the glutathione S-transferases (GSTs). To maximize sequence identity and minimize gaps in the alignment, a hybrid approach is used that takes advantage of the increased homology found between DM11 and domain I of the sheep blowfly theta class GST (residues 1-79) and domain II of the human alpha class GST (residues 81-222). The resulting structure has C alpha root mean square deviations of 1.16 A in domain I and 1.83 A in domain II from the template GSTs, which compare well to those seen in other GST inter-class comparisons. The model is further applied to explore the structural basis for substrate binding and catalysis. A conserved network of hydrogen bonds is described that binds glutathione to the G site, placing the thiol group in a suitable location for nucleophilic attack of dichloromethane. A mechanism is proposed that involves activation through a hydrogen bond interaction between Ser12 and glutathione, similar to that found in the theta-GSTs. The model also demonstrates how aromatic residues in the hydrophobic site (H site) could play a role in promoting catalysis: His116 and Trp117 are ideally situated to accept a growing negative charge on a chlorine of dichloromethane, stabilizing displacement. This scheme is consistent with experimental results of single-point mutations and comparisons with other GST structures and mechanisms.
Marsh
A
A
Department of Medicinal Chemistry and Minnesota Supercomputer Institute, University of Minnesota, Minneapolis 55455, USA.
Ferguson
D M
DM
D000595:Amino Acid Sequence; D000818:Animals; D006088:Gram-Negative Aerobic Bacteria / Q000201:enzymology*; D006801:Humans; D008190:Lyases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D008190:Lyases; C045224:dichloromethane dehalogenase