PDBsum entry: 1w1q

Oxidoreductase

PDB id: 1w1q

Contents

Protein chain

479 a.a. *

Ligands

FAD

ZIP

NAG ×3

NAG-NAG

Waters ×287

* Residue conservation analysis

PDB id:

1w1q

Name:

Oxidoreductase

Title:

Plant cytokinin dehydrogenase in complex with isopentenyladenine

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:

1.80Å R-factor: 0.206 R-free: 0.221

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

Protein chain

Q9T0N8  (CKX1_MAIZE) -  Cytokinin dehydrogenase 1

Seq: 534 a.a.

Struc: 479 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.5.99.12 - Cytokinin dehydrogenase.
• Reaction: N₆-dimethylallyladenine + acceptor + H₂O = adenine + 3-methylbut-2- enal + reduced acceptor

N(6)-dimethylallyladenine (Bound ligand (Het Group name = ZIP) corresponds exactly) + 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 

• 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 š . 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.