NAD+-enzyme binding mode and structure, overview. The NAD+-binding pocket is constituted by seven loops (beta7-alpha4, beta8-alpha5, beta10-alpha7, beta11-beta12, alpha8-beta13, alpha9-alpha10, and alpha11-beta16) and four alpha-helices (alpha4, alpha6, alpha7, and alpha10). The adenine ring is stabilized in the hydrophobic pocket that is formed by Phe151, Pro211, Ala212, Phe229, Val235 and Leu239, and a hydrogen bond with Ser215 also contributes to the binding of the ring. Residues Lys178, Glu181, and Pro211 constitute a suitable space for binding of the ribose ring, and stabilize the 2'-hydroxyl-group of the ring. The formation of the ribose ring binding site does not seem to be large enough to accommodate the phosphorylated ribose ring. Therefore the enzyme shows poor activity with NADP+ as a cofactor. The diphosphate moiety is stabilized by residues Asn331, Arg333, and Arg334 through directly and water-mediated hydrogen bond networks. Residues Arg334 and Glu384 stabilize the ribose moiety of NAD+, and the nicotinamide ring is stabilized by residues Gln160 and Glu253 by hydrogen bonding
preferred cofactor, residues chosen for generating the NAD+ binding pocket library are shown using the crystal structure of KGSADH complexed with NAD+ (PDB ID 5X5U), overview
low ALDH activity has been reported to cause intracellular accumulation of highly toxic 3-hydroxypropionaldehyde (3-HPA) seriously hampering the cell growth
alpa-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH) can catalyze the ALDH reaction forming 3-hydroxypropionate, but it is not its physiological substrate
molecular docking simulations of AbKGSADH with 2-oxoglutaric semialdehyde (alpha-KGSA) and succinate semialdehyde (SSA). Molecular docking simulations reveal that these two substrates fit well into the somewhat positively charged substrate binding pocket. The aldehyde-groups of these substrates, which are the sites of enzyme reaction, are located in the same place around the catalytic residues. The aldehyde-group of alpha-KGSA is stabilized by Gln160 and Arg163 through hydrogen bonds, and two catalytic residues, Glu253 and Cys287, also assist the binding of the molecule. The 4'-oxo-group of alpha-KGSA is stabilized by hydrogen bonds with Arg281, and the carboxyl-group of the molecule is stabilized by Glu106 and Gln160. The substrate binding pocket is also formed by several hydrophobic residues, such as Phe156, Val286, Ile288, Pro444, and Phe450, which seem to contribute to the stabilization of the hydrophobic part of alpha-KGSA. The binding of SSA is similar to that of alpha-KGSA, however, the stabilization of the carboxyl-group of SSA is quite different. Arg281, a residue that is involved in the stabilization of the 4'-oxo-group of alpha-KGSA, forms a hydrogen bond with the carboxyl-group of SSA instead. These observations explain how AbKGSADH can accommodate both alpha-KGSA and SSA as real substrates
molecular docking simulations of AbKGSADH with 2-oxoglutaric semialdehyde (alpha-KGSA) and succinate semialdehyde (SSA). Molecular docking simulations reveal that these two substrates fit well into the somewhat positively charged substrate binding pocket. The aldehyde-groups of these substrates, which are the sites of enzyme reaction, are located in the same place around the catalytic residues. The aldehyde-group of alpha-KGSA is stabilized by Gln160 and Arg163 through hydrogen bonds, and two catalytic residues, Glu253 and Cys287, also assist the binding of the molecule. The 4'-oxo-group of alpha-KGSA is stabilized by hydrogen bonds with Arg281, and the carboxyl-group of the molecule is stabilized by Glu106 and Gln160. The substrate binding pocket is also formed by several hydrophobic residues, such as Phe156, Val286, Ile288, Pro444, and Phe450, which seem to contribute to the stabilization of the hydrophobic part of alpha-KGSA. The binding of SSA is similar to that of alpha-KGSA, however, the stabilization of the carboxyl-group of SSA is quite different. Arg281, a residue that is involved in the stabilization of the 4'-oxo-group of alpha-KGSA, forms a hydrogen bond with the carboxyl-group of SSA instead. These observations explain how AbKGSADH can accommodate both alpha-KGSA and SSA as real substrates
although there are two AbKGSADH molecules in the asymmetric unit of our present structures, the tetrameric structure can be easily generated by one of the two folds from the P4322 crystallographic symmetry operation, structure modeling, overview. The monomeric structure of AbKGSADH consists of three domains: two core domains and one oligomerization domain (OGD). The core domains consist of the N-terminal domain (NTD) (Met1-Arg123 and Val145-Leu253) and the C-terminal domain (CTD) (Gly254-Pro469). The NTD is composed of seven alpha-helices (alpha1-alpha7) and nine beta-strands (beta1-beta4 and beta7-beta11), and forms the NAD(P)-binding Rossmann fold, where seven beta-strands (beta1-beta2 and beta7-beta11) form a large beta-sheet packed in the middle of the domain and other two beta-strands (beta3-beta4) are located on the surface of the domain. The three alpha-helices (alpha1, alpha6 and alpha7) and the four alpha-helices (alpha2-alpha5) occupy both sides of the central beta-sheet. The CTD consists of seven alpha-helices (alpha8-alpha14) and seven beta-strands (beta12-beta18). Seven beta-strands are also packed as a large beta-sheet in the middle of the domain. Six alpha-helices surround the central beta-sheet and one alpha-helix (alpha14) is located between the NTD and the OGD. The OGD (Val124-Pro144 and Tyr470-Val481) has two long beta-strands (beta6 and beta19) and one short beta-strand (beta5), which are packed in a line and protrude from the NTD
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme in apoform and in complex with NAD+, sitting-drop vapor diffusion method, mixing of 0.001 ml of 60 mg/ml protein in 40 mM Tris-HCl pH 8.0 with 0.001 ml of reservoir solution containing 16% PEG 3350, 0.1 M sodium cacodylate, pH 6.5, and 0.2 M magnesium chloride hexahydrate, equilibration against 0.05 ml of reservoir solution, X-ray diffraction structure determination and analysis at 2.25 A and 2.30 A resolution, molecular replacement structure modeling using the structure of succinic semialdehyde dehydrogenase (SSADH) from Homo sapiens (PDB ID 2W8R) as a search model for the apoenzyme, and the crystal structure of the apoform of AbKGSADH as a template for the NAD+-complexed AbKGSADH structure
random mutagenesis, the mutant shows reduced activity with 3-hydroxypropionaldehyde and altered cofactor kinetics compared to the wild-type enzyme, no activity with NADP+
random mutagenesis, the mutant shows reduced activity with 3-hydroxypropionaldehyde and altered cofactor kinetics compared to the wild-type enzyme, no activity with NADP+
random mutagenesis, the mutant shows increased activity with 3-hydroxypropionaldehyde and altered cofactor kinetics compared to the wild-type enzyme, no activity with NADP+
random mutagenesis, the mutant shows strongly increased activity with 3-hydroxypropionaldehyde and altered cofactor kinetics compared to the wild-type enzyme
engineering of alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense for prodduction of 3-hydroxypropanoate (HP) from 3-hydroxypropionaldehyde (3-HPA). A directed evolutionary strategy is adopted as the engineering approach for modifying the substrate-binding sites of KGSADH. The residues in the binding sites for the substrates, 3-HPA and NAD+, are randomized, and the resulting libraries are screened for higher activity. Isolated KGSADH variants have significantly lower Km values for both the substrates. The enzymes also show higher substrate specificities for aldehyde and NAD+, less inhibition by NADH, and greater resistance to inactivation by 3-HPA than the wild-type enzyme. A recombinant Pseudomonas denitrificans strain expressing one of the engineered KGSADH variants exhibits less accumulation of 3-HPA, decreased levels of inactivation of the enzymes, and higher cell growth than that expressing the wild-type KGSADH. The flask culture of the Pseudomonas denitrificans strain with the mutant KGSADH results in about 40% increase of 3-HP titer (53 mM) compared with that using the wild-type enzyme (37 mM). Mutant structure modeling, overview
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3)-T1 by nickel affinity chromatography, gel filtration, and ultrafiltration
recombinant N-terminally His6-tagged wild-type and mutant KGSADH enzymes from Escherichia coli strain DH10beta by nickel affinity chromatography and ultrafiltration
alpha-ketoglutaric semialdehyde dehydrogenase isozymes involved in metabolic pathways of D-glucarate, D-galactarate, and hydroxy-L-proline. Molecular and metabolic convergent evolution