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PDBsum entry 1w1o

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protein ligands links
Oxidoreductase PDB id
1w1o
Jmol
Contents
Protein chain
479 a.a. *
Ligands
FAD
NAG ×3
NAG-NAG
Waters ×627
* Residue conservation analysis
PDB id:
1w1o
Name: Oxidoreductase
Title: Native cytokinin dehydrogenase
Structure: Cytokinin dehydrogenase 1. Chain: a. Synonym: cytokinin oxidase 1, cko 1. Engineered: yes
Source: Zea mays. Maize. Organism_taxid: 4577. Expressed in: pichia pastoris. Expression_system_taxid: 4922
Resolution:
1.70Å     R-factor:   0.199     R-free:   0.215
Authors: E.Malito,A.Mattevi
Key ref:
E.Malito et al. (2004). Structures of Michaelis and product complexes of plant cytokinin dehydrogenase: implications for flavoenzyme catalysis. J Mol Biol, 341, 1237-1249. PubMed id: 15321719 DOI: 10.1016/j.jmb.2004.06.083
Date:
23-Jun-04     Release date:   26-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9T0N8  (CKX1_MAIZE) -  Cytokinin dehydrogenase 1
Seq:
Struc:
 
Seq:
Struc:
534 a.a.
479 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.5.99.12  - Cytokinin dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N6-dimethylallyladenine + acceptor + H2O = adenine + 3-methylbut-2- enal + reduced acceptor
N(6)-dimethylallyladenine
+ acceptor
+ H(2)O
= adenine
+ 3-methylbut-2- enal
+ reduced acceptor
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.06.083 J Mol Biol 341:1237-1249 (2004)
PubMed id: 15321719  
 
 
Structures of Michaelis and product complexes of plant cytokinin dehydrogenase: implications for flavoenzyme catalysis.
E.Malito, A.Coda, K.D.Bilyeu, M.W.Fraaije, A.Mattevi.
 
  ABSTRACT  
 
Cytokinins form a diverse class of compounds that are essential for plant growth. Cytokinin dehydrogenase has a major role in the control of the levels of these plant hormones by catalysing their irreversible oxidation. The crystal structure of Zea mays cytokinin dehydrogenase displays the same two-domain topology of the flavoenzymes of the vanillyl-alcohol oxidase family but its active site cannot be related to that of any other family member. The X-ray analysis reveals a bipartite architecture of the catalytic centre, which consists of a funnel-shaped region on the protein surface and an internal cavity lined by the flavin ring. A pore with diameter of about 4A connects the two active-site regions. Snapshots of two critical steps along the reaction cycle were obtained through the structural analysis of the complexes with a slowly reacting substrate and the reaction product, which correspond to the states immediately before (Michaelis complex) and after (product complex) oxidation has taken place. The substrate displays a "plug-into-socket" binding mode that seals the catalytic site and precisely positions the carbon atom undergoing oxidation in close contact with the reactive locus of the flavin. A polarising H-bond between the substrate amine group and an Asp-Glu pair may facilitate oxidation. Substrate to product conversion results in small atomic movements, which lead to a planar conformation of the reaction product allowing double-bond conjugation. These features in the mechanism of amine recognition and oxidation differ from those observed in other flavin-dependent amine oxidases.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Shape and architecture of the active site of CKX. (a) Close-up view of the protein surface in the region surrounding the active site in approximately the same orientation as in Figure 3. The picture outlines the internal cavity located in front of the flavin ring (yellow) connected through a pore to the outside surface. The oxidised N 6 -isopentenyladenine ligand is shown in black. The cavity and surface calculations were done using a probe radius of 1.4 A . 31 (b) View of the CKX monomer surface. The isopentenyl substituent is buried inside the internal cavity, whereas the adenine ring sticks
Figure 7.
Figure 7. Stereochemistry of the interactions between the flavin ring and the reactive N10--C11 amino group (Figure 1) of the substrate with reference to the N 6 - benzyladenine complex.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 1237-1249) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19438712 D.P.Heuts, N.S.Scrutton, W.S.McIntire, and M.W.Fraaije (2009).
What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.
  FEBS J, 276, 3405-3427.  
19459938 F.Forneris, R.Orru, D.Bonivento, L.R.Chiarelli, and A.Mattevi (2009).
ThermoFAD, a Thermofluor-adapted flavin ad hoc detection system for protein folding and ligand binding.
  FEBS J, 276, 2833-2840.  
19436049 M.Smehilová, P.Galuszka, K.D.Bilyeu, P.Jaworek, M.Kowalska, M.Sebela, M.Sedlárová, J.T.English, and I.Frébort (2009).
Subcellular localization and biochemical comparison of cytosolic and secreted cytokinin dehydrogenase enzymes from maize.
  J Exp Bot, 60, 2701-2712.  
18953357 A.Winkler, A.Lyskowski, S.Riedl, M.Puhl, T.M.Kutchan, P.Macheroux, and K.Gruber (2008).
A concerted mechanism for berberine bridge enzyme.
  Nat Chem Biol, 4, 739-741.
PDB codes: 3d2d 3d2h 3d2j
17886275 E.Bae, C.A.Bingman, E.Bitto, D.J.Aceti, and G.N.Phillips (2008).
Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase.
  Proteins, 70, 303-306.
PDB codes: 2exr 2q4w
16600599 A.Mattevi (2006).
To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes.
  Trends Biochem Sci, 31, 276-283.  
16807830 T.Werner, I.Köllmer, I.Bartrina, K.Holst, and T.Schmülling (2006).
New insights into the biology of cytokinin degradation.
  Plant Biol (Stuttg), 8, 371-381.  
17030803 Z.D.Fang, J.G.Laskey, S.Huang, K.D.Bilyeu, R.O.Morris, F.J.Schmidt, and J.T.English (2006).
Combinatorially selected defense peptides protect plant roots from pathogen infection.
  Proc Natl Acad Sci U S A, 103, 18444-18449.  
16154992 C.H.Huang, W.L.Lai, M.H.Lee, C.J.Chen, A.Vasella, Y.C.Tsai, and S.H.Liaw (2005).
Crystal structure of glucooligosaccharide oxidase from Acremonium strictum: a novel flavinylation of 6-S-cysteinyl, 8alpha-N1-histidyl FAD.
  J Biol Chem, 280, 38831-38838.
PDB codes: 1zr6 2axr
16332885 M.H.Lee, W.L.Lai, S.F.Lin, C.S.Hsu, S.H.Liaw, and Y.C.Tsai (2005).
Structural characterization of glucooligosaccharide oxidase from Acremonium strictum.
  Appl Environ Microbiol, 71, 8881-8887.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.