Maize cytokinin oxidase/dehydrogenase complexed with the allenic cytokinin analog HA-8

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 

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This is version 2.1 of the entry. See complete history


Mechanism-based inhibitors of cytokinin oxidase/dehydrogenase attack FAD cofactor

Kopecny, D.Sebela, M.Briozzo, P.Spichal, L.Houba-Herin, N.Masek, V.Joly, N.Madzak, C.Anzenbacher, P.Laloue, M.

(2008) J Mol Biol 380: 886-899

  • DOI: https://doi.org/10.1016/j.jmb.2008.05.044
  • Primary Citation of Related Structures:  
    3BW7, 3C0P

  • PubMed Abstract: 

    Cytokinin oxidases/dehydrogenases (CKOs) mediate catabolic regulation of cytokinin levels in plants. Several substrate analogs containing an unsaturated side chain were studied for their possible inhibitory effect on maize CKO (ZmCKO1) by use of various bioanalytical methods. Two allenic derivatives, N(6)-(buta-2,3-dienyl)adenine (HA-8) and N(6)-(penta-2,3-dienyl)adenine (HA-1), were identified as strong mechanism-based inhibitors of the enzyme. Despite exhaustive dialysis, the enzyme remained inhibited. Conversely, substrate analogs with a triple bond in the side chain were much weaker inactivators. The crystal structures of recombinant ZmCKO1 complexed with HA-1 or HA-8 were solved to 1.95 A resolution. Together with Raman spectra of the inactivated enzyme, it was revealed that reactive imine intermediates generated by oxidation of the allenic inhibitors covalently bind to the flavin adenine dinucleotide (FAD) cofactor. The binding occurs at the C4a atom of the isoalloxazine ring of FAD, the planarity of which is consequently disrupted. All the compounds under study were also analyzed for binding to the Arabidopsis cytokinin receptors AHK3 and AHK4 in a bacterial receptor assay and for cytokinin activity in the Amaranthus bioassay. HA-1 and HA-8 were found to be good receptor ligands with a significant cytokinin activity. Nevertheless, due to their ability to inactivate CKO in the desired time intervals or developmental stages, they both represent attractive compounds for physiological studies, as the inhibition mechanism of HA-1 and HA-8 is mainly FAD dependent.

  • Organizational Affiliation

    Laboratoire de Biologie Cellulaire, INRA, Route de Saint-Cyr, F-78026 Versailles Cedex, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokinin dehydrogenase 1516Zea maysMutation(s): 3 
Gene Names: CKX1ZmCKO1
Find proteins for Q9T0N8 (Zea mays)
Explore Q9T0N8 
Go to UniProtKB:  Q9T0N8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9T0N8
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
B, C, D
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 250.7α = 90
b = 50.2β = 93.8
c = 51.2γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2011-11-09
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary