PMID: 9188739Jun 1, 1997Paper

Knowledge-based modeling of a bacterial dichloromethane dehalogenase

Proteins
A Marsh, D M Ferguson

Abstract

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: ...Continue Reading

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Citations

Apr 23, 2011·Journal of the American Chemical Society·Peter W Y ChanEmil F Pai
Mar 13, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Svenja T Lohner, Alfred M Spormann
Nov 20, 2008·The FEBS Journal·Nerino AllocatiCarmine Di Ilio
Dec 14, 2005·Environmental Microbiology·Marcell NikolauszMatthias Kästner
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May 10, 2003·Chemosphere·Karl Heinz van Pée, Susanne Unversucht

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