3NG7

Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family

Kachalova, G.Decker, K.Holt, A.Bartunik, H.D.

(2011) Proc.Natl.Acad.Sci.USA 108: 4800-4805

  • DOI: 10.1073/pnas.1016684108

  • PubMed Abstract: 
  • FAD-linked oxidases constitute a class of enzymes which catalyze dehydrogenation as a fundamental biochemical reaction, followed by reoxidation of reduced flavin. Here, we present high-resolution crystal structures showing the flavoenzyme 6-hydroxy-l ...

    FAD-linked oxidases constitute a class of enzymes which catalyze dehydrogenation as a fundamental biochemical reaction, followed by reoxidation of reduced flavin. Here, we present high-resolution crystal structures showing the flavoenzyme 6-hydroxy-l-nicotine oxidase in action. This enzyme was trapped during catalytic degradation of the native substrate in a sequence of discrete reaction states corresponding to the substrate-reduced enzyme, a complex of the enzyme with the intermediate enamine product and formation of the final aminoketone product. The inactive d-stereoisomer binds in mirror symmetry with respect to the catalytic axis, revealing absolute stereospecificity of hydrogen transfer to the flavin. The structural data suggest deprotonation of the substrate when bound at the active site, an overall binary complex mechanism and oxidation by direct hydride transfer. The amine nitrogen has a critical role in the dehydrogenation step and may activate carbocation formation at the α-carbon via delocalization from the lone pair to σ* C(α)-H. Enzymatically assisted hydrolysis of the intermediate product occurs at a remote (P site) cavity. Substrate entry and product exit follow different paths. Structural and kinetic data suggest that substrate can also bind to the reduced enzyme, associated with slower reoxidation as compared to the rate of reoxidation of free enzyme. The results are of general relevance for the mechanisms of flavin amine oxidases.


    Related Citations: 
    • 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


    Organizational Affiliation

    Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, 22607 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
HNL
Query on HNL

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Download CCD File 
X
5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol
6-hydroxy-L-nicotine
C10 H14 N2 O
ATRCOGLZUCICIV-VIFPVBQESA-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
FAD
Query on FAD

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Download CCD File 
X
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 
  • Space Group: P 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 163.771α = 90.00
b = 163.771β = 90.00
c = 163.771γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
MAR345data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-26
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description