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 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 U S A 108: 4800-4805

  • DOI: https://doi.org/10.1073/pnas.1016684108
  • Primary Citation of Related Structures:  
    3NG7

  • 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-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.


  • Organizational Affiliation

    Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-hydroxy-L-nicotine oxidaseA [auth X]431Paenarthrobacter nicotinovoransMutation(s): 0 
Gene Names: 6-hlno
EC: 1.5.3.5
UniProt
Find proteins for Q93NH4 (Paenarthrobacter nicotinovorans)
Explore Q93NH4 
Go to UniProtKB:  Q93NH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93NH4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth X]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GP7
Query on GP7

Download Ideal Coordinates CCD File 
D [auth X](1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(pentadecanoyloxy)methyl]ethyl (12E)-hexadeca-9,12-dienoate
C36 H68 N O8 P
NMIBJXZODRRZEA-NTSPIXPOSA-N
HNK
Query on HNK

Download Ideal Coordinates CCD File 
E [auth X]5-[(2R)-1-methylpyrrolidin-2-yl]pyridin-2-ol
C10 H14 N2 O
ATRCOGLZUCICIV-SECBINFHSA-N
HNL
Query on HNL

Download Ideal Coordinates CCD File 
B [auth X]5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol
C10 H14 N2 O
ATRCOGLZUCICIV-VIFPVBQESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.771α = 90
b = 163.771β = 90
c = 163.771γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-26
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description