3D9G

Nitroalkane oxidase: wild type crystallized in a trapped state forming a cyanoadduct with FAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of intermediates in the nitroalkane oxidase reaction.

Heroux, A.Bozinovski, D.M.Valley, M.P.Fitzpatrick, P.F.Orville, A.M.

(2009) Biochemistry 48: 3407-3416

  • DOI: 10.1021/bi8023042
  • Primary Citation of Related Structures:  

  • 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 resoluti ...

    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.


    Related Citations: 
    • Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase.
      Fitzpatrick, P.F.,Bozinovski, D.M.,Heroux, A.,Shaw, P.G.,Valley, M.P.,Orville, A.M.
      (2007) Biochemistry 46: 13800
    • Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.
      Nagpal, A.,Valley, M.P.,Fitzpatrick, P.F.,Orville, A.M.
      (2006) Biochemistry 45: 1138


    Organizational Affiliation

    Department of Biology, Brookhaven National Laboratory, Upton, New York 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitroalkane oxidase
A, B, C, D
438Fusarium oxysporumMutation(s): 0 
EC: 1.7.3.1
Find proteins for Q8X1D8 (Fusarium oxysporum)
Go to UniProtKB:  Q8X1D8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CNX
Query on CNX

Download SDF File 
Download CCD File 
A, B, C, D
heptanenitrile
1-cyanohexane
C7 H13 N
SDAXRHHPNYTELL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.256α = 90.00
b = 109.256β = 90.00
c = 343.945γ = 120.00
Software Package:
Software NamePurpose
CBASSdata collection
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2014-04-23
    Type: Database references
  • Version 1.3: 2018-03-21
    Type: Data collection