3NN6

Crystal structure of inhibitor-bound in active centre 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure analysis of free and substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans.

Kachalova, G.S.Bourenkov, G.P.Mengesdorf, T.Schenk, S.Maun, H.R.Burghammer, M.Riekel, C.Decker, K.Bartunik, H.D.

(2010) J.Mol.Biol. 396: 785-799

  • DOI: 10.1016/j.jmb.2009.12.009
  • Primary Citation of Related Structures:  
  • Also Cited By: 3NG7

  • PubMed Abstract: 
  • The pathway for oxidative degradation of nicotine in Arthrobacter nicotinovorans includes two genetically and structurally unrelated flavoenzymes, 6-hydroxy-L-nicotine oxidase (6HLNO) and 6-hydroxy-D-nicotine oxidase, which act with absolute stereosp ...

    The pathway for oxidative degradation of nicotine in Arthrobacter nicotinovorans includes two genetically and structurally unrelated flavoenzymes, 6-hydroxy-L-nicotine oxidase (6HLNO) and 6-hydroxy-D-nicotine oxidase, which act with absolute stereospecificity on the L- and D-forms, respectively, of 6-hydroxy-nicotine. We solved the crystal structure of 6HLNO at 1.95 A resolution by combined isomorphous/multiple-wavelength anomalous dispersion phasing. The overall structure of each subunit of the 6HLNO homodimer and the folds of the individual domains are closely similar as in eukaryotic monoamine oxidases. Unexpectedly, a diacylglycerophospholipid molecule was found to be non-covalently bound to each protomer of 6HLNO. The fatty acid chains occupy hydrophobic channels that penetrate deep into the interior of the substrate-binding domain of each subunit. The solvent-exposed glycerophosphate moiety is located at the subunit-subunit interface. We further solved the crystal structure of a complex of dithionite-reduced 6HLNO with the natural substrate 6-hydroxy-L-nicotine at 2.05 A resolution. The location of the substrate in a tight cavity suggests that the binding geometry of this unproductive complex may be closely similar as under oxidizing conditions. The observed orientation of the bound substrate relative to the isoalloxazine ring of the flavin adenine dinucleotide cofactor is suitable for hydride-transfer dehydrogenation at the carbon atom that forms the chiral center of the substrate molecule. A comparison of the substrate-binding modes of 6HLNO and 6-hydroxy-D-nicotine oxidase, based on models of complexes with the D-substrate, suggests an explanation for the stereospecificity of both enzymes. The two enzymes are proposed to orient the enantiomeric substrates in mirror symmetry with respect to the plane of the flavin.


    Related Citations: 
    • Crystal structure analysis of free and substrate-bound 6-hydroxy-L-nicotine from Arthrobacter nicotinovorans
      Kachalova, G.S.,Bourenkov, G.P.,Mengesdorf, T.,Schenk, S.,Maun, H.R.,Burghammer, M.,Riekel, C.,Decker, K.,Bartunik, H.D.
      (2010) J.Mol.Biol. 396: 785


    Organizational Affiliation

    Max-Planck Unit for Structural Molecular Biology, MPG-ASMB c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-hydroxy-L-nicotine oxidase
X
431Paenarthrobacter nicotinovoransMutation(s): 0 
Gene Names: 6-hlno
EC: 1.5.3.5
Find proteins for Q93NH4 (Paenarthrobacter nicotinovorans)
Go to UniProtKB:  Q93NH4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FB0
Query on FB0

Download SDF File 
Download CCD File 
X
(2R,3S,4S)-5-({[(acetylcarbamoyl)amino]methyl}[(3S,4R)-6-amino-3,4-dimethylhexyl]amino)-2,3,4-trihydroxypentyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
C27 H49 N9 O15 P2
GXAQOPQBDYJNIO-CCGDWWFSSA-N
 Ligand Interaction
GP7
Query on GP7

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Download CCD File 
X
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate
1-pentadecanoyl-2-hexadecanoyl-sn-glycero-3-phosphoethanolamine
C36 H68 N O8 P
NMIBJXZODRRZEA-NTSPIXPOSA-N
 Ligand Interaction
HNK
Query on HNK

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Download CCD File 
X
5-[(2R)-1-methylpyrrolidin-2-yl]pyridin-2-ol
6-hydroxy-D-nicotine
C10 H14 N2 O
ATRCOGLZUCICIV-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • Space Group: P 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 164.184α = 90.00
b = 164.184β = 90.00
c = 164.184γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MAR345data collection
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description