7KHO image
Deposition Date 2020-10-21
Release Date 2021-02-10
Last Version Date 2023-10-18
Entry Detail
PDB ID:
7KHO
Keywords:
Title:
NicA2 variant N462V in complex with (S)-nicotine
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.69 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Amine oxidase
Gene (Uniprot):nicA2
Mutations:N462V
Chain IDs:A, B, C, D
Chain Length:490
Number of Molecules:4
Biological Source:Pseudomonas putida S16
Primary Citation
Fast Kinetics Reveals Rate-Limiting Oxidation and the Role of the Aromatic Cage in the Mechanism of the Nicotine-Degrading Enzyme NicA2.
Biochemistry 60 259 273 (2021)
PMID: 33464876 DOI: 10.1021/acs.biochem.0c00855

Abstact

In Pseudomonas putida, the flavoprotein nicotine oxidoreductase (NicA2) catalyzes the oxidation of (S)-nicotine to N-methyl-myosmine, which is nonenzymatically hydrolyzed to pseudooxynicotine. Structural analysis reveals a monoamine oxidase (MAO)-like fold with a conserved FAD-binding domain and variable substrate-binding domain. The flavoenzyme has a unique variation of the classic aromatic cage with flanking residue pair W427/N462. Previous mechanistic studies using O2 as the oxidizing substrate show that NicA2 has a low apparent Km of 114 nM for (S)-nicotine with a very low apparent turnover number (kcat of 0.006 s-1). Herein, the mechanism of NicA2 was analyzed by transient kinetics. Single-site variants of W427 and N462 were used to probe the roles of these residues. Although several variants had moderately higher oxidase activity (7-12-fold), their reductive half-reactions using (S)-nicotine were generally significantly slower than that of wild-type NicA2. Notably, the reductive half-reaction of wild-type NicA2 is 5 orders of magnitude faster than the oxidative half-reaction with an apparent pseudo-first-order rate constant for the reaction of oxygen similar to kcat. X-ray crystal structures of the N462V and N462Y/W427Y variants complexed with (S)-nicotine (at 2.7 and 2.3 Å resolution, respectively) revealed no significant active-site rearrangements. A second substrate-binding site was identified in N462Y/W427Y, consistent with observed substrate inhibition. Together, these findings elucidate the mechanism of a flavoenzyme that preferentially oxidizes tertiary amines with an efficient reductive half-reaction and a very slow oxidative half-reaction when O2 is the oxidizing substrate, suggesting that the true oxidizing agent is unknown.

Legend

Protein

Chemical

Disease

Primary Citation of related structures