The role of enzyme distortion in the single displacement mechanism of family 19 chitinases.
By using molecular dynamics simulations, we have examined the binding of a hexaNAG substrate and two potential hydrolysis intermediates (an oxazoline ion and an oxocarbenium ion) to a family 19 barley chitinase. We find the hexaNAG substrate binds with all sugars in a chair conformation, unlike the family 18 chitinase which causes substrate distortion. Glu 67 is in a position to protonate the anomeric oxygen linking sugar residues D and E whereas Asn 199 serves to hydrogen bond with the C2' N-acetyl group of sugar D, thus preventing the formation of an oxazoline ion intermediate. In addition, Glu 89 is part of a flexible loop region allowing a conformational change to occur within the active site to bring the oxocarbenium ion intermediate and Glu 89 closer by 4-5 A. A hydrolysis product with inversion of the anomeric configuration occurs because of nucleophilic attack by a water molecule that is coordinated by Glu 89 and Ser 120. Issues important for the design of inhibitors specific to family 19 chitinases over family 18 chitinases also are discussed.
Brameld
K A
KA
Materials and Process Simulation Center, Beckman Institute (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Goddard
W A
WA
D000595:Amino Acid Sequence; D001665:Binding Sites; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D002686:Chitin / Q000737:chemistry* / Q000378:metabolism*; D002688:Chitinases / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D018698:Glutamic Acid; D001467:Hordeum / Q000201:enzymology; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D012984:Software; D013379:Substrate Specificity
D002686:Chitin; D018698:Glutamic Acid; D002688:Chitinases