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Shanru He,Chenyuan Yuan,Xue Bai,Tingting Bu,Jie Zhang,Lulu Wang,Chunshan Quan,Yongbin Xu 한국구조생물학회 2022 Biodesign Vol.10 No.2
Anaerobic gram-negative bacterium Fusobacterium nucleatum (F. nucleatum) has long been found to cause opportunistic infections and has recently been implicated in colorectal cancer. In F. nucleatum, YggS (FnYggS) is an important part of bacterial cell walls and belongs to the COG0325 gene family. In this study, YggS from FnYggS was successfully expressed and purified using Ni-NTA affinity and gel-filtration chromatography. The protein crystal was obtained and diffracted to a resolution of 2.08 Å. The preliminary crystallographic analysis suggested that FnYggS crystal belongs to the monoclinic space group P21 with a = 37.93 Å, b = 146.38 Å, and c = 74.13 Å, α = γ = 90.00° and β = 93.36°. The asymmetric unit contained approximately three monomer of FnYggS, giving a crystal volume per mass (VM) of 2.64 Å3 Da–1 and a solvent content of 53.50%.
Shanru He,Yongbin Xu 한국구조생물학회 2023 Biodesign Vol.11 No.3
3-ketoacyl-acyl carrier protein (ACP) reductase is a vital enzyme in the biosynthesis of fatty acids in bacteria and plants. It assumes a critical role in the elongation process of fatty acids. The enzyme’s primary function is to catalyze the reduction of a 3-ketoacyl-ACP intermediate, forming a fully saturated acyl-ACP. This saturated acyl-ACP can subsequently elongate within the fatty acid synthesis pathway. This study successfully expressed and purified FnFabG from Fusobacterium nucleatum using Ni-NTA affinity and gel-filtration chromatography. The protein crystal was obtained and diffracted to a resolution of 2.7 Å. The preliminary crystallographic analysis suggested that FnFabG crystal belongs to the monoclinic space group P41212 with a = b = 111.56 Å and c = 88.69 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of FnFabG, giving a solvent content of 78.33%.
Xue Bai,Jing Lan,Shanru He,Tingting Bu,Jie Zhang,Lulu Wang,Chunshan Quan,Ki Hyun Nam,Nam-Chul Ha,Yongbin Xu 한국구조생물학회 2022 Biodesign Vol.10 No.2
Fusobacterium nucleatum is a dangerous pathogen, and it has been linked to a variety of health problems, including cancer, periodontal disease, and pregnancy complications. F. nucleatum butanol dehydrogenase (FnYqdH) is a group of dehydrogenase enzymes that facilitate interconversion between butyraldehyde and butanol at the expenditure of a cofactor NAD (P)H. In this study, FnYqdH was successfully expressed and purified using Ni-NTA affinity, Q anionexchange, and gel-filtration chromatography. The protein crystal was obtained and diffracted to a resolution of 2.0 Å. The crystal belonged to the orthorhombic space group of I222, with unit-cell parameters of a = 64.77, b = 78.85, and c = 215.22 Å. The Matthews coefficient and solvent content were estimated to be 3.19 Å3 Da–1 and 61.49%, respectively, assuming that the asymmetric unit contained only one recombinant protein molecule. Size-exclusion chromatography suggested that FnYqdH prefers to exist as a dimer in the solution.
Jie Zhang,Xue Bai,Shanru He,Yongbin Xu 한국구조생물학회 2023 Biodesign Vol.11 No.3
Candida auris is a new fungus that poses a serious global health threat due to its resistance to multiple antifungal medications, making treatment challenging. Aldo-keto reductase (AKR) represents a versatile superfamily of enzymes that play pivotal roles in the phase I metabolism of various metabolic and detoxification processes. In this study, AKR from C. auris (CaAldO) was successfully expressed and purified using Ni-NTA affinity, Q anion exchange, and gel-filtration chromatography. The protein crystal was obtained and diffracted to a resolution of 1.95 Å. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters of a = 71.65, b = 91.15, and c = 227.66 Å. The Matthews coefficient and solvent content were estimated to be 2.32 Å3 Da–1 and 47.00%, respectively, assuming the asymmetric unit contained four recombinant protein molecules.
Jie Zhang,Yuanyuan Chen,Tingting Bu,Xue Bai,Shanru He,Lulu Wang,Chunshan Quan,Yongbin Xu 한국구조생물학회 2022 Biodesign Vol.10 No.3
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous and highly abundant glycolytic enzyme. It plays a pivotal role for the energy and carbon metabolism of most organisms including industrial bacteria. It catalyzes the two step oxidative phosphorylation of D-glyceraldehyde-3-phosphate into 1,3-bisphosphoglycerate using inorganic phosphate and nicotinamide adenine dinucleotide (NAD+) as cofactor. In this study, GAPDH from C. beijerinckii (CbGAPDH) was successfully expressed and purified using Ni-NTA affinity, Q anion-exchange, and gel-filtration chromatography. The protein crystal was obtained and diffracted to a resolution of 1.60 Å. The crystal belonged to the hexagonal space group P6222, with unit-cell parameters of a = 120.6, b = 120.6, and c = 122.1 Å. The Matthews coefficient and solvent content were estimated to be 3.50 Å3 Da–1 and 64.90%, respectively, assuming that the asymmetric unit contained only one recombinant protein molecule.
Jie Zhang,Tingting Bu,Yuanyuan Chen,Xue Bai,Shanru He,Yongbin Xu 한국구조생물학회 2022 Biodesign Vol.10 No.4
Clostridium beijerinckii is a promising industrial microorganism for its ability to produce butanol, acetone, and isopropanol using a wide range of substrates, including pentoses, hexoses, and starch, via fermentation. The ubiquitous and highly abundant glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is essential for most organisms’ energy and carbon metabolism, which plays a critical role in some industrial bacteria. It catalyzes the simultaneous oxidation and phosphorylation of D-glyceraldehyde-3-phosphate into 1,3-bisphosphoglycerate in the presence of inorganic phosphate and nicotinamide adenine dinucleotide (NAD+). We determined the crystal structure of the GAPDH from C. beijerinckii (C. beijerinckii GAPDH). C. beijerinckii GAPDH consists of an α-β-α domain which shares an evolutionarily conserved fold consisting of two juxtaposed domains, an N-terminal NAD+-binding domain (NBD) and a C-terminal catalytic domain (CD). These findings provide insight into the molecular mechanism of action and cofactorbinding of this important industrial bacterial enzyme.