3S1F

Asp169Glu mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site.

Kopecny, D.Koncitikova, R.Popelka, H.Briozzo, P.Vigouroux, A.Kopecna, M.Zalabak, D.Sebela, M.Skopalova, J.Frebort, I.Morera, S.

(2016) FEBS J 283: 361-377

  • DOI: 10.1111/febs.13581
  • Primary Citation of Related Structures:  
    3S1C, 3S1D, 3S1E, 3S1F, 4ML8, 4MLA, 4O95, 4OAL

  • PubMed Abstract: 
  • Cytokinins are hormones that regulate plant development and their environmental responses. Their levels are mainly controlled by the cytokinin oxidase/dehydrogenase (CKO), which oxidatively cleaves cytokinins using redox-active electron acceptors. CKO belongs to the group of flavoproteins with an 8α-N1-histidyl FAD covalent linkage ...

    Cytokinins are hormones that regulate plant development and their environmental responses. Their levels are mainly controlled by the cytokinin oxidase/dehydrogenase (CKO), which oxidatively cleaves cytokinins using redox-active electron acceptors. CKO belongs to the group of flavoproteins with an 8α-N1-histidyl FAD covalent linkage. Here, we investigated the role of seven active site residues, H105, D169, E288, V378, E381, P427 and L492, in substrate binding and catalysis of the CKO1 from maize (Zea mays, ZmCKO1) combining site-directed mutagenesis with kinetics and X-ray crystallography. We identify E381 as a key residue for enzyme specificity that restricts substrate binding as well as quinone electron acceptor binding. We show that D169 is important for catalysis and that H105 covalently linked to FAD maintains the enzyme's structural integrity, stability and high rates with electron acceptors. The L492A mutation significantly modulates the cleavage of aromatic cytokinins and zeatin isomers. The high resolution X-ray structures of ZmCKO1 and the E381S variant in complex with N6-(2-isopentenyl)adenosine reveal the binding mode of cytokinin ribosides. Those of ZmCKO2 and ZmCKO4a contain a mobile domain, which might contribute to binding of the N9 substituted cytokinins.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytokinin dehydrogenase 1A516Zea maysMutation(s): 1 
Gene Names: CKX1
EC: 1.5.99.12
UniProt
Find proteins for Q9T0N8 (Zea mays)
Explore Q9T0N8 
Go to UniProtKB:  Q9T0N8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9T0N8
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZIP
Query on ZIP

Download Ideal Coordinates CCD File 
D [auth A]N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE
C10 H13 N5
HYVABZIGRDEKCD-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 250.17α = 90
b = 50.67β = 94.02
c = 51.21γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata 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: 2012-05-23
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2015-12-23
    Changes: Database references
  • Version 1.3: 2016-04-20
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary