Adenine binding mode is a key factor in triggering the early release of NADH in coenzyme A-dependent methylmalonate semialdehyde dehydrogenase.
Structural dynamics associated with cofactor binding have been shown to play key roles in the catalytic mechanism of hydrolytic NAD(P)-dependent aldehyde dehydrogenases (ALDH). By contrast, no information is available for their CoA-dependent counterparts. We present here the first crystal structure of a CoA-dependent ALDH. The structure of the methylmalonate semialdehyde dehydrogenase (MSDH) from Bacillus subtilis in binary complex with NAD(+) shows that, in contrast to what is observed for hydrolytic ALDHs, the nicotinamide ring is well defined in the electron density due to direct and H(2)O-mediated hydrogen bonds with the carboxamide. The structure also reveals that a conformational isomerization of the NMNH is possible in MSDH, as shown for hydrolytic ALDHs. Finally, the adenine ring is substantially more solvent-exposed, a result that could be explained by the presence of a Val residue at position 229 in helix α(F) that reduces the depth of the binding pocket and the absence of Gly-225 at the N-terminal end of helix α(F). Substitution of glycine for Val-229 and/or insertion of a glycine residue at position 225 resulted in a significant decrease of the rate constant associated with the dissociation of NADH from the NADH/thioacylenzyme complex, thus demonstrating that the weaker stabilization of the adenine ring is a key factor in triggering the early NADH release in the MSDH-catalyzed reaction. This study provides for the first time structural insights into the mechanism whereby the cofactor binding mode is responsible at least in part for the different kinetic behaviors of the hydrolytic and CoA-dependent ALDHs.
Unité Mixte de Recherche CNRS-Université de Lorraine 7214 AREMS, ARN-RNP Structure-Fonction-Maturation, Enzymologie Moléculaire et Structurale, Faculté de Médecine, Biopôle, 9 Avenue de la Forêt de Haye, BP 184, 54506 Vandœuvre-lès-Nancy, France.
Raphaël
R
Bchini
Hélène
H
Dubourg-Gerecke
Sophie
S
Rahuel-Clermont
André
A
Aubry
Guy
G
Branlant
Claude
C
Didierjean
François
F
Talfournier
D000225:Adenine / Q000737:chemistry* / Q000378:metabolism; D001412:Bacillus subtilis / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D006868:Hydrolysis; D007700:Kinetics; D050646:Methylmalonate-Semialdehyde Dehydrogenase (Acylating) / Q000737:chemistry* / Q000378:metabolism; D009249:NADP / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D013329:Structure-Activity Relationship
D001426:Bacterial Proteins; D009249:NADP; D050646:Methylmalonate-Semialdehyde Dehydrogenase (Acylating); D000225:Adenine