3D9D

Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane

Summary for 3D9D

• Entry DOI: 10.2210/pdb3d9d/pdb
• Related: 2c0u 2c12 2reh 2zaf 3D9E 3D9F 3D9G
• Descriptor: Nitroalkane oxidase, FLAVIN-ADENINE DINUCLEOTIDE, 1-nitrohexane, ... (5 entities in total)
• Functional Keywords: oxidoreductase flavoenzyme, nitroalkane, acyl-coa dehydrogenase, long cell edge, fad, inhibitor, flavoprotein, oxidoreductase
• Biological source: Fusarium oxysporum
• Total number of polymer chains: 4
• Total formula weight: 196751.91

Authors

Heroux, A.,Bozinovski, D.M.,Valley, M.P.,Fitzpatrick, P.F.,Orville, A.M. (deposition date: 2008-05-27, release date: 2009-04-07, Last modification date: 2023-11-01)

Primary citation

Heroux, A.,Bozinovski, D.M.,Valley, M.P.,Fitzpatrick, P.F.,Orville, A.M.
Crystal structures of intermediates in the nitroalkane oxidase reaction.
Biochemistry, 48:3407-3416, 2009

PubMed Abstract: The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 A resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes [Valley, M. P., and Fitzpatrick, P. F. (2003) J. Am. Chem. Soc. 125, 8738-8739]. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped [Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066]. The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

PubMed: 19265437
DOI: 10.1021/bi8023042

Experimental method

X-RAY DIFFRACTION (2.1 Å)