8yvr

From Proteopedia

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with 1-deoxynojirimycin

Structural highlights

8yvr is a 3 chain structure with sequence from Flavobacterium johnsoniae UW101. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KJASE_FLAJ1 Glycosidase that specifically hydrolyzes kojibiose to beta-glucose and glucose (PubMed:34728215). Also hydrolyzes, with lower catalytic efficiency, longer kojioligosaccharides (from kojitriose to kojipentaose) and shorter oligosaccharides produced by the degradation of dextran-containing alpha-1,2 branches (PubMed:34728215). Probably acts on alpha-(1->2)-glucosyl isomaltooligosaccharides (PubMed:37269952). Shows weak activity with nigerose but has no activity toward p-nitrophenyl alpha-glucopyranoside, which is a general substrate of exo-acting alpha-glucoside hydrolases (PubMed:34728215). Has a strict specificity for alpha-1,2-glucosidic linkages (PubMed:34728215). Catalyzes the hydrolytic reaction via an anomer-inverting mechanism (PubMed:34728215).^[1] ^[2]

Publication Abstract from PubMed

Glycoside hydrolase family 65 (GH65) includes glycoside hydrolases active on various alpha-glucosides. We previously demonstrated that the GH65 enzyme from Flavobacterium johnsoniae (FjGH65A) is a kojibiose hydrolase and determined its 3-dimensional structure. In this study, the effects of glucosidase inhibitors on FjGH65A and their complex structures were analyzed to elucidate their inhibition mechanism. FjGH65A was competitively inhibited by 1-deoxynojirimycin (DNJ) and noncompetitively inhibited by castanospermine (CSP) with Ki values of 2.95 and 3.69 microm, respectively. The crystal structures of FjGH65A complexed with the inhibitors indicated that DNJ was bound to subsite -1 of FjGH65A, while CSP was bound to subsites -1 and +1 of FjGH65A. Compared with the glucose complex structure, the conformation of Tyr337 was changed in the CSP complex structure. These results provide new structural insights into the mechanism of inhibition against GH65 alpha-glucoside hydrolases.

Structural insights into the inhibition mechanism of glucosidase inhibitors toward kojibiose hydrolase belonging to glycoside hydrolase family 65.,Nakamura S, Miyazaki T Biosci Biotechnol Biochem. 2024 Dec 23;89(1):72-79. doi: 10.1093/bbb/zbae158. PMID:39533825^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nakamura S, Nihira T, Kurata R, Nakai H, Funane K, Park EY, Miyazaki T. Structure of a bacterial alpha-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases. J Biol Chem. 2021 Oct 30;297(6):101366. doi: 10.1016/j.jbc.2021.101366. PMID:34728215 doi:http://dx.doi.org/10.1016/j.jbc.2021.101366
↑ Nakamura S, Kurata R, Tonozuka T, Funane K, Park EY, Miyazaki T. Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J Biol Chem. 2023 Jun 1:104885. PMID:37269952 doi:10.1016/j.jbc.2023.104885
↑ Nakamura S, Miyazaki T. Structural insights into the inhibition mechanism of glucosidase inhibitors toward kojibiose hydrolase belonging to glycoside hydrolase family 65. Biosci Biotechnol Biochem. 2024 Dec 23;89(1):72-79. PMID:39533825 doi:10.1093/bbb/zbae158