title: A general correction to catalytic rates determined for nonprocessive exo-depolymerases acting on both substrate and product in the initial-rate measurement.
abstract: We recently reported on the kinetics of the polygalacturonase TtGH28 acting on trimer and dimer substrates. When the starting substrate for hydrolysis is the trimer, the product dimer is also subject to hydrolysis, resulting in discrepancies when either the concentration of dimer or monomer product is used for analysis of trimer hydrolysis. Here, we derive a method for determining catalytic rates of exo-hydrolases acting on trimer (and higher order) substrates when products may also be substrates for hydrolysis and show how this correction may be applied for TtGH28.
authors.affiliation: USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604, USA.
authors.forename: J Rose
authors.initials: JR
authors.lastname: Stoller
authors.affiliation: USDA-ARS-Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
authors.forename: Kurt
authors.initials: K
authors.lastname: Wagschal
authors.affiliation: USDA-ARS-Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA.
authors.forename: Charles C
authors.initials: CC
authors.lastname: Lee
authors.affiliation: USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604, USA. Electronic address: douglas.jordan@ars.usda.gov.
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Jordan
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D004187:Disaccharides / Q000378:metabolism*; D006603:Hexuronic Acids / Q000378:metabolism*; D006868:Hydrolysis; D007700:Kinetics; D011096:Polygalacturonase / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity; D013400:Sugar Acids / Q000378:metabolism*; D016963:Thermus thermophilus / Q000201:enzymology*; D014312:Trisaccharides / Q000378:metabolism*
chemical_list: D004187:Disaccharides; D006603:Hexuronic Acids; D013400:Sugar Acids; D014312:Trisaccharides; C007819:galacturonic acid; C065008:O-galactopyranosyluronic acid-(1-4)-O-galactopyranosyluronic acid-(1-4)-galactopyranosyluronic acid; D011096:Polygalacturonase; C090179:digalacturonic acid
keywords: Enzyme kinetics; Exo-hydrolase; Glycoside hydrolase family 28; Nonprocessive; Polygalacturonase