Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of the strict specificity of a bacterial GH31 α-1,3-glucosidase for nigerooligosaccharides.
Journal, issue, pages	J Biol Chem, Vol. 298, Issue 5, Page 101827, Year 2022
Publish date	Mar 12, 2022
Authors	Marina Ikegaya / Toshio Moriya / Naruhiko Adachi / Masato Kawasaki / Enoch Y Park / Takatsugu Miyazaki /
PubMed Abstract	Carbohydrate-active enzymes are involved in the degradation, biosynthesis, and modification of carbohydrates and vary with the diversity of carbohydrates. The glycoside hydrolase (GH) family 31 is ...Carbohydrate-active enzymes are involved in the degradation, biosynthesis, and modification of carbohydrates and vary with the diversity of carbohydrates. The glycoside hydrolase (GH) family 31 is one of the most diverse families of carbohydrate-active enzymes, containing various enzymes that act on α-glycosides. However, the function of some GH31 groups remains unknown, as their enzymatic activity is difficult to estimate due to the low amino acid sequence similarity between characterized and uncharacterized members. Here, we performed a phylogenetic analysis and discovered a protein cluster (GH31_u1) sharing low sequence similarity with the reported GH31 enzymes. Within this cluster, we showed that a GH31_u1 protein from Lactococcus lactis (LlGH31_u1) and its fungal homolog demonstrated hydrolytic activities against nigerose [α-D-Glcp-(1→3)-D-Glc]. The k/K values of LlGH31_u1 against kojibiose and maltose were 13% and 2.1% of that against nigerose, indicating that LlGH31_u1 has a higher specificity to the α-1,3 linkage of nigerose than other characterized GH31 enzymes, including eukaryotic enzymes. Furthermore, the three-dimensional structures of LlGH31_u1 determined using X-ray crystallography and cryogenic electron microscopy revealed that LlGH31_u1 forms a hexamer and has a C-terminal domain comprising four α-helices, suggesting that it contributes to hexamerization. Finally, crystal structures in complex with nigerooligosaccharides and kojibiose along with mutational analysis revealed the active site residues involved in substrate recognition in this enzyme. This study reports the first structure of a bacterial GH31 α-1,3-glucosidase and provides new insight into the substrate specificity of GH31 enzymes and the physiological functions of bacterial and fungal GH31_u1 members.
External links	J Biol Chem / PubMed:35293315 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.75 - 2.73 Å
Structure data	32571 7wlg EMDB-32571, PDB-7wlg: Cryo-EM structure of GH31 alpha-1,3-glucosidase from Lactococcus lactis subsp. cremoris Method: EM (single particle) / Resolution: 2.73 Å PDB-7wj9: Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase, P21 space group Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-7wja: Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase, P6322 space group Method: X-RAY DIFFRACTION / Resolution: 1.85 Å PDB-7wjb: Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase in complex with glucose Method: X-RAY DIFFRACTION / Resolution: 2.0 Å PDB-7wjc: Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerose Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-7wjd: Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerotriose Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-7wje: Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerotetraose Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-7wjf: Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with kojibiose Method: X-RAY DIFFRACTION / Resolution: 1.8 Å
Chemicals	ChemComp-XYL: Xylitol / Xylitol ChemComp-EDO: 1,2-ETHANEDIOL / Ethylene glycol ChemComp-HOH: WATER / Water ChemComp-GLC: alpha-D-glucopyranose / Glucose ChemComp-BGC: beta-D-glucopyranose / Glucose
Source	lactococcus lactis subsp. cremoris mg1363 (lactic acid bacteria)
Keywords	HYDROLASE / nigerose / glucose / glycoside hydrolase / GH31 / carbohydrate / TIM-barrel / hexamer / kojibiose