Binding of β-D-glucosides and β-D-mannosides by rice and barley β-D-glycosidases with distinct substrate specificities

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dc.contributor.authorKuntothom, T.
dc.contributor.authorRaab, M.
dc.contributor.authorTvaroska, I.
dc.contributor.authorFort, S.
dc.contributor.authorPengthaisong, S.
dc.contributor.authorCanada, J.
dc.contributor.authorCalle, L.
dc.contributor.authorJiminez-Barbero, J.
dc.contributor.authorCairns, J.
dc.contributor.authorHrmova, M.
dc.date.issued2010
dc.description.abstractPredominantly, rice Os3BGlu7 operates as a β-d-glucosidase (EC 3.2.1.21), while barley HvBII acts as a β-d-mannosidase (EC 3.2.1.25). Saturation transfer difference nuclear magnetic resonance (STD NMR) and transferred nuclear Overhauser effect (trNOE) spectroscopy in conjunction with quantum mechanics/molecular mechanics (QM/MM) modeling and docking at the 6-31+G* level were used to investigate binding of S- and O-linked gluco- and manno-configured aryl-β-d-glycosides to Os3BGlu7 and HvBII. Kinetic analyses with 4-nitrophenyl β-d-thioglucoside (4NP-S-Glc) and 4-nitrophenyl β-d-thiomannoside (4NP-S-Man) indicated that the inhibitions were competitive with apparent K(i) constants of 664 and 710 μM for Os3BGlu7 and 95 and 266 μM for HvBII, respectively. The STD NMR and trNOESY experiments revealed that 4NP-S-Glc and 4NP-S-Man bound weakly in (4)C(1) conformations to Os3BGlu7; 4NP-S-Glc adopted (3)S(5) (B(3,O)) or (1)S(3) ((1,4)B) conformations, and 4NP-S-Man preferred (4)C(1) geometry, when bound to HvBII. The QM modeling and docking, based on GLIDE scores, predicted that 4NP-O-Glc, 4NP-O-Man, and 4NP-S-Man bound preferentially in (1)S(3) geometries to both enzymes, contrary to 4NP-S-Glc that could also adopt a (4)C(1) conformation, although in a "flipped-down" ring position. The experimental and computational data suggested that in glycoside recognition and substrate specificity of Os3BGlu7 and HvBII, a combination of the following determinants is likely to play key roles: (i) the inherent conformational and spatial flexibilities of gluco- and manno-configured substrates in the enzymes' active sites, (ii) the subtle differences in the spatial disposition of active site residues and their capacities to form interactions with specific groups of substrates, and (iii) the small variations in the charge distributions and shapes of the catalytic sites.
dc.description.statementofresponsibilityTeerachai Kuntothom, Michal Raab, Igor Tvaroska, Sebastien Fort, Salila Pengthaisong, Javier Cañada, Luis Calle, Jesús Jiménez-Barbero, James R. Ketudat Cairns, and Maria Hrmova
dc.identifier.citationBiochemistry, 2010; 49(40):8779-8793
dc.identifier.doi10.1021/bi101112c
dc.identifier.issn0006-2960
dc.identifier.issn1520-4995
dc.identifier.orcidHrmova, M. [0000-0002-3545-0605]
dc.identifier.urihttp://hdl.handle.net/2440/62079
dc.language.isoen
dc.publisherAmer Chemical Soc
dc.relation.grantARC
dc.rightsCopyright © 2010 American Chemical Society
dc.source.urihttps://doi.org/10.1021/bi101112c
dc.subjectHordeum
dc.subjectbeta-Glucosidase
dc.subjectbeta-Mannosidase
dc.subjectGlycosides
dc.subjectMannosides
dc.subjectNuclear Magnetic Resonance, Biomolecular
dc.subjectProtein Binding
dc.subjectSubstrate Specificity
dc.subjectModels, Molecular
dc.subjectOryza
dc.titleBinding of β-D-glucosides and β-D-mannosides by rice and barley β-D-glycosidases with distinct substrate specificities
dc.title.alternativeBinding of beta-D-glucosides and beta-D-mannosides by rice and barley beta-D-glycosidases with distinct substrate specificities
dc.typeJournal article
pubs.publication-statusPublished

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