Knowledge-based modeling of a bacterial dichloromethane dehalogenase

Amanda Marsh, David M Ferguson

Research output: Contribution to journalArticle

24 Citations (Scopus)

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 θ class GST (residues 1-79) and domain II of the human α class GST (residues 81-222). The resulting structure has Cα root mean square deviations of 1.16 Å in domain I and 1.83 in domain II from the template GSTs, which compare well to those seen in other GST interclass 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 θ-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.

Original languageEnglish (US)
Pages (from-to)217-226
Number of pages10
JournalProteins: Structure, Function and Genetics
Volume28
Issue number2
DOIs
StatePublished - Jul 14 1997

Fingerprint

Glutathione Transferase
Methylene Chloride
Catalysis
Methylophilus
Glutathione
Hydrogen
Hydrogen bonds
Structural Models
Chlorine
Point Mutation
Sulfhydryl Compounds
dichloromethane dehalogenase
Sheep
Chemical activation
Substrates

Keywords

  • DM11
  • Glutathione S-transferase
  • Homology modeling
  • Theta class

Cite this

Knowledge-based modeling of a bacterial dichloromethane dehalogenase. / Marsh, Amanda; Ferguson, David M.

In: Proteins: Structure, Function and Genetics, Vol. 28, No. 2, 14.07.1997, p. 217-226.

Research output: Contribution to journalArticle

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