6ik8

Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,6-galactobiose

spinqualitylabelsall models 6ik8, resolution 2.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6ik8 is a 2 chain structure with sequence from Solanum lycopersicum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.8Å Ligands: GAL, NAG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function O81100_SOLLC Publication Abstract from PubMed MAIN CONCLUSION: TBG4 recognize multiple linkage types substrates due to having a spatially wide subsite + 1. This feature allows the degradation of AGI, AGII, and AGP leading to the fruit ripening. beta-galactosidase (EC 3. 2. 1. 23) catalyzes the hydrolysis of beta-galactan and release of D-galactose. Tomato has at least 17 beta-galactosidases (TBGs), of which, TBG 4 is responsible for fruit ripening. TBG4 hydrolyzes not only beta-1,4-bound galactans, but also beta-1,3- and beta-1,6-galactans. In this study, we compared each enzyme-substrate complex using X-ray crystallography, ensemble refinement, and docking simulation to understand the broad substrate-specificity of TBG4. In subsite - 1, most interactions were conserved across each linkage type of galactobioses; however, some differences were seen in subsite + 1, owing to the huge volume of catalytic pocket. In addition to this, docking simulation indicated TBG4 to possibly have more positive subsites to recognize and hydrolyze longer galactans. Taken together, our results indicated that during tomato fruit ripening, TBG4 plays an important role by degrading arabinogalactan I (AGI), arabinogalactan II (AGII), and the carbohydrate moiety of arabinogalactan protein (AGP). Substrate-recognition mechanism of tomato beta-galactosidase 4 using X-ray crystallography and docking simulation.,Matsuyama K, Kondo T, Igarashi K, Sakamoto T, Ishimaru M Planta. 2020 Oct 3;252(4):72. doi: 10.1007/s00425-020-03481-4. PMID:33011862 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Galactosidase 3D structures

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