Crystal structure of the NADP+-dependent aldehyde dehydrogenase from Vibrio harveyi: structural implications for cofactor specificity and affinity

Abstract

Aldehyde dehydrogenase from the bioluminescent bacterium, Vibrio harveyi, catalyses the oxidation of long-chain aliphatic aldehydes to acids. The enzyme is unique compared with other forms of aldehyde dehydrogenase in that it exhibits a very high specificity and affinity for the cofactor NADP(+). Structural studies of this enzyme and comparisons with other forms of aldehyde dehydrogenase provide the basis for understanding the molecular features that dictate these unique properties and will enhance our understanding of the mechanism of catalysis for this class of enzyme. The X-ray structure of aldehyde dehydrogenase from V. harveyi has been solved to 2.5-A resolution as a partial complex with the cofactor NADP(+) and to 2. 1-A resolution as a fully bound 'holo' complex. The cofactor preference exhibited by different forms of the enzyme is predominantly determined by the electrostatic environment surrounding the 2'-hydroxy or the 2'-phosphate groups of the adenosine ribose moiety of NAD(+) or NADP(+), respectively. In the NADP(+)-dependent structures the presence of a threonine and a lysine contribute to the cofactor specificity. In the V. harveyi enzyme an arginine residue (Arg-210) contributes to the high cofactor affinity through a pi stacking interaction with the adenine ring system of the cofactor. Further differences between the V. harveyi enzyme and other aldehyde dehydrogenases are seen in the active site, in particular a histidine residue which is structurally conserved with phosphorylating glyceraldehyde-3-phosphate dehydrogenase. This may suggest an alternative mechanism for activation of the reactive cysteine residue for nucleophilic attack.

Crystal Structure of a Novel Shikimate Dehydrogenase from Haemophilus influenzae

“…Such an interaction is important for discriminating between NAD ϩ and NADP ϩ (21, 22). In addition, its alkyl side chain stacks with the adenine ring, and such interactions have been shown to improve the binding affinity for the nucleotide (23). This observation, i.e.…”

A Novel α-Ketoglutaric Semialdehyde Dehydrogenase

“…Therefore, it is likely that this novel ALDH class is characterized as a unique NADP ϩ -dependent enzyme. Recently, the crystallographic study of V. harveyi ALDH revealed that the overall structural fold and location of most key amino acid residues in the active site are the same as those found in other ALDHs despite their low sequential homologies (38).…”

Conserved Catalytic Residues of the ALDH1L1 Aldehyde Dehydrogenase Domain Control Binding and Discharging of the Coenzyme

“…After the hydride transfer, the reduced nicotinamide ring must exit the catalytic site to allow for the accessibility of a water molecule, which hydrolyzes the acyl-sulfur bond releasing the product. In agreement with this mechanism, numerous crystal structures of ALDH revealed two common conformations of the coenzyme, depending on its oxidation state: the extended ("hydride transfer") conformation of NAD(P) ϩ , with the nicotinamide ring positioned close to Cys-302; and the contracted ("hydrolysis") conformation of NAD(P)H, with the nicotinamide ring found outside of the catalytic site or disordered (4,5,7,10,25,27,30). The mechanism by which ALDHs sense the oxidation state of the bound coenzyme and control its conformation is not fully understood.…”