4MLA | pdb_00004mla

Structure of maize cytokinin oxidase/dehydrogenase 2 (ZmCKO2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.222 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4MLA

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1111/febs.13581
  • Primary Citation 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. 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
    • Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 115.89 kDa 
  • Atom Count: 8,004 
  • Modeled Residue Count: 937 
  • Deposited Residue Count: 1,002 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytokinin oxidase 2
A, B
501Zea maysMutation(s): 0 
Gene Names: cko2
EC: 1.5.99.12
UniProt
Find proteins for Q709Q5 (Zea mays)
Explore Q709Q5 
Go to UniProtKB:  Q709Q5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ709Q5
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
BA [auth B],
C [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
CA [auth B],
K [auth A],
OA [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
EA [auth B]
G [auth A]
I [auth A]
J [auth A]
W [auth A]
EA [auth B],
G [auth A],
I [auth A],
J [auth A],
W [auth A],
Y [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
AA [auth B]
D [auth A]
DA [auth B]
E [auth A]
F [auth A]
AA [auth B],
D [auth A],
DA [auth B],
E [auth A],
F [auth A],
FA [auth B],
GA [auth B],
H [auth A],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
P [auth A],
PA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
X [auth A],
Z [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.72α = 90
b = 181.89β = 90
c = 196.96γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary