PDBsum entry 2c12

Oxidoreductase

PDB id: 2c12

Contents

Protein chains

(+ 0 more) 430 a.a. *

Ligands

FAD ×6

GOL ×15

SPM ×4

PE4 ×2

Waters ×1117

* Residue conservation analysis

PDB id:

2c12

Name:

Oxidoreductase

Title:

Crystal structure of nitroalkane oxidase in complex with spermine, a competitive inhibitor

Structure:

Nitroalkane oxidase. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Fusarium oxysporum. Organism_taxid: 5507. Atcc: 695. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.07Å R-factor: 0.190 R-free: 0.225

Authors:

A.Nagpal,M.P.Valley,P.F.Fitzpatrick,A.M.Orville

Key ref:

A.Nagpal et al. (2006). Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover. Biochemistry, 45, 1138-1150. PubMed id: 16430210 DOI: 10.1021/bi051966w

Date:

10-Sep-05 Release date: 01-Feb-06

Protein chains

Q8X1D8  (NAO_FUSOX) -  Nitroalkane oxidase from Fusarium oxysporum

Seq: 439 a.a.

Struc: 430 a.a.

Enzyme reactions

• Enzyme class: E.C.1.7.3.1 - nitroalkane oxidase.
• Reaction:
  1. a primary nitroalkane + O2 + H2O = an aldehyde + nitrite + H2O2 + H⁺
  2. a secondary nitroalkane + O2 + H2O = a ketone + nitrite + H2O2 + H⁺
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi051966w

Biochemistry 45:1138-1150 (2006)

PubMed id: 16430210

Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.

A.Nagpal, M.P.Valley, P.F.Fitzpatrick, A.M.Orville.

ABSTRACT

Nitroalkane oxidase (NAO) from Fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of H(2)O(2) and nitrite. The flavoenzyme is a new member of the acyl-CoA dehydrogenase (ACAD) family, but it does not react with acyl-CoA substrates. We present the 2.2 A resolution crystal structure of NAO trapped during the turnover of nitroethane as a covalent N5-FAD adduct (ES*). The homotetrameric structure of ES* was solved by MAD phasing with 52 Se-Met sites in an orthorhombic space group. The electron density for the N5-(2-nitrobutyl)-1,5-dihydro-FAD covalent intermediate is clearly resolved. The structure of ES was used to solve the crystal structure of oxidized NAO at 2.07 A resolution. The c axis for the trigonal space group of oxidized NAO is 485 A, and there are six subunits (1(1)/(2) holoenzymes) in the asymmetric unit. Four of the active sites contain spermine (EI), a weak competitive inhibitor, and two do not contain spermine (E(ox)). The active-site structures of E(ox), EI, and ES* reveal a hydrophobic channel that extends from the exterior of the protein and terminates at Asp402 and the N5 position on the re face of the FAD. Thus, Asp402 is in the correct position to serve as the active-site base, where it is proposed to abstract the alpha proton from neutral nitroalkane substrates. The structures for NAO and various members of the ACAD family overlay with root-mean-square deviations between 1.7 and 3.1 A. The homologous region typically spans more than 325 residues and includes Glu376, which is the active-site base in the prototypical member of the ACAD family. However, NAO and the ACADs exhibit differences in hydrogen-bonding patterns between the respective active-site base, substrate molecules, and FAD. These likely differentiate NAO from the homologues and, consequently, are proposed to result in the unique reaction mechanism of NAO.