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 analysis of pathogenic mutations targeting Glu427 of ALDH7A1, the hot spot residue of pyridoxine-dependent epilepsy.
Journal, issue, pages	J Inherit Metab Dis, Vol. 43, Issue 3, Page 635-644, Year 2020
Publish date	Dec 1, 2019
Authors	Adrian R Laciak / David A Korasick / Kent S Gates / John J Tanner /
PubMed Abstract	Certain loss-of-function mutations in the gene encoding the lysine catabolic enzyme aldehyde dehydrogenase 7A1 (ALDH7A1) cause pyridoxine-dependent epilepsy (PDE). Missense mutations of Glu427, ...Certain loss-of-function mutations in the gene encoding the lysine catabolic enzyme aldehyde dehydrogenase 7A1 (ALDH7A1) cause pyridoxine-dependent epilepsy (PDE). Missense mutations of Glu427, especially Glu427Gln, account for ~30% of the mutated alleles in PDE patients, and thus Glu427 has been referred to as a mutation hot spot of PDE. Glu427 is invariant in the ALDH superfamily and forms ionic hydrogen bonds with the nicotinamide ribose of the NAD cofactor. Here we report the first crystal structures of ALDH7A1 containing pathogenic mutations targeting Glu427. The mutant enzymes E427Q, Glu427Asp, and Glu427Gly were expressed in Escherichia coli and purified. The recombinant enzymes displayed negligible catalytic activity compared to the wild-type enzyme. The crystal structures of the mutant enzymes complexed with NAD were determined to understand how the mutations impact NAD binding. In the E427Q and E427G structures, the nicotinamide mononucleotide is highly flexible and lacks a defined binding pose. In E427D, the bound NAD adopts a "retracted" conformation in which the nicotinamide ring is too far from the catalytic Cys residue for hydride transfer. Thus, the structures revealed a shared mechanism for loss of function: none of the variants are able to stabilise the nicotinamide of NAD in the pose required for catalysis. We also show that these mutations reduce the amount of active tetrameric ALDH7A1 at the concentration of NAD tested. Altogether, our results provide the three-dimensional molecular structural basis of the most common pathogenic variants of PDE and implicate strong (ionic) hydrogen bonds in the aetiology of a human disease.
External links	J Inherit Metab Dis / PubMed:31652343 / PubMed Central
Methods	SAS (X-ray synchrotron) / X-ray diffraction
Resolution	1.75 - 2.15 Å
Structure data	SASDGH4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 at 1.2 mg/mL Method: SAXS/SANS SASDGJ4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 at 2.3 mg/mL Method: SAXS/SANS SASDGK4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 at 4.7 mg/mL Method: SAXS/SANS SASDGL4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399Q at 1.1 mg/mL Method: SAXS/SANS SASDGM4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399Q at 2.1 mg/mL Method: SAXS/SANS SASDGN4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399Q at 4.3 mg/mL Method: SAXS/SANS SASDGP4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399D at 1.4 mg/mL Method: SAXS/SANS SASDGQ4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399D at 2.9 mg/mL Method: SAXS/SANS SASDGR4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399D at 5.7 mg/mL Method: SAXS/SANS SASDGS4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399G at 1.6 mg/mL Method: SAXS/SANS SASDGT4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399G at 3.2 mg/mL Method: SAXS/SANS SASDGU4: Human alpha-aminoadipic semialdehyde dehydrogenase (ALDH)7A1 E399G at 6.5 mg/mL Method: SAXS/SANS PDB-6o4i: Structure of ALDH7A1 mutant E399D complexed with alpha-aminoadipate Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-6o4k: Structure of ALDH7A1 mutant E399Q complexed with NAD Method: X-RAY DIFFRACTION / Resolution: 2.06 Å PDB-6o4l: Structure of ALDH7A1 mutant E399D complexed with NAD Method: X-RAY DIFFRACTION / Resolution: 1.85 Å PDB-6u2x: Structure of ALDH7A1 mutant E399G complexed with NAD Method: X-RAY DIFFRACTION / Resolution: 2.15 Å
Chemicals	ChemComp-UN1: 2-AMINOHEXANEDIOIC ACID ChemComp-EDO: 1,2-ETHANEDIOL ChemComp-HOH: WATER ChemComp-NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADYM ChemComp-CL*: Unknown entry
Source	homo sapiens (human)
Keywords	OXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / LYSINE CATABOLISM