9vd8

Structure of a truncated loopA mutant from the human gut flora K. grimontii Apg in complex with glucose

spinqualitylabelsall models 9vd8, resolution 2.39Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9vd8 is a 1 chain structure with sequence from Klebsiella grimontii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.39Å Ligands: GLC Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The clinical efficacy of the antidiabetic drug acarbose is hampered by degradation by the acarbose-preferred glucosidase (Apg) from K. grimontii TD1. Understanding the catalytic mechanism of Apg can aid the design of next-generation hypoglycemic pharmaceuticals acarbose analogs. Here, we determine several crystal structures of Apg to identify the catalytic residues and the ligand-binding pocket of Apg. Structural analyses and computational modeling reveal D448 as the active nucleophile, contrasting with prior studies that assumed D336 to be the nucleophile. In addition to E373 proposed as the proton donor in previous reports, we find that R334 might be an alternative proton donor. Our experimental and computational analyses indicate the two-ring product acarviosine is the two-step hydrolyzed product, where the second hydrolysis is the rate-limiting step. Additionally, further investigation of the acarbose analogs acarstatins A and B that are resistant to Apg is conducted by computational analysis. Overall, our studies provide perspectives into the intricacies of Apg's catalytic mechanism, contributing to the design of next-generation hypoglycemic pharmaceuticals. Molecular insights of acarbose metabolization catalyzed by acarbose-preferred glucosidase.,Huang J, Shen Z, Xiao X, Wang L, Zhang J, Zhou J, Gu Y Nat Commun. 2025 Aug 22;16(1):7839. doi: 10.1038/s41467-025-62855-y. PMID:40846838 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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