PDBsum entry: 2qkn

Oxidoreductase

PDB id: 2qkn

Contents

Protein chain

496 a.a. *

Ligands

NAG ×2

NAG-NAG ×3

FAD

245-245

GOL

Waters ×295

* Residue conservation analysis

PDB id:

2qkn

Name:

Oxidoreductase

Title:

Crystal structure of maize cytokinin oxidase/dehydrogenasE C with phenylurea inhibitor cppu

Structure:

Cytokinin dehydrogenase 1. Chain: a. Synonym: cytokinin oxidase 1. Cko 1. Cox 1. Zmckx. Cytokini oxidase/dehydrogenase. Engineered: yes

Source:

Zea mays. Maize. Organism_taxid: 4577. Variant: nobilis. Gene: ckx1. Expressed in: yarrowia lipolytica. Expression_system_taxid: 4952.

Resolution:

2.15Å R-factor: 0.191 R-free: 0.231

Authors:

P.Briozzo

Key ref:

D.Kopečný et al. (2010). Phenyl- and benzylurea cytokinins as competitive inhibitors of cytokinin oxidase/dehydrogenase: A structural study. Biochimie, 92, 1052-1062. PubMed id: 20478354 DOI: 10.1016/j.biochi.2010.05.006

Date:

11-Jul-07 Release date: 01-Jul-08

Protein chain

Q9T0N8  (CKX1_MAIZE) -  Cytokinin dehydrogenase 1

Seq: 534 a.a.

Struc: 496 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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 + acceptor + H(2)O = adenine + 3-methylbut-2- enal (Bound ligand (Het Group name = GOL) matches with 50.00% similarity) + 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 

• Cellular component: extracellular region (2 terms)
• Biological process: oxidation-reduction process (2 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1016/j.biochi.2010.05.006

Biochimie 92:1052-1062 (2010)

PubMed id: 20478354

Phenyl- and benzylurea cytokinins as competitive inhibitors of cytokinin oxidase/dehydrogenase: A structural study.

D.Kopečný, P.Briozzo, H.Popelková, M.Sebela, R.Končitíková, L.Spíchal, J.Nisler, C.Madzak, I.Frébort, M.Laloue, N.Houba-Hérin.

ABSTRACT

Cytokinin oxidase/dehydrogenase (CKO) is a flavoenzyme, which irreversibly degrades the plant hormones cytokinins and thereby participates in their homeostasis. Several synthetic cytokinins including urea derivatives are known CKO inhibitors but structural data explaining enzyme-inhibitor interactions are lacking. Thus, an inhibitory study with numerous urea derivatives was undertaken using the maize enzyme (ZmCKO1) and the crystal structure of ZmCKO1 in a complex with N-(2-chloro-pyridin-4-yl)-N -phenylurea (CPPU) was solved. CPPU binds in a planar conformation and competes for the same binding site with natural substrates like N(6)-(2-isopentenyl)adenine (iP) and zeatin (Z). Nitrogens at the urea backbone are hydrogen bonded to the putative active-site base Asp169. Subsequently, site-directed mutagenesis of L492 and E381 residues involved in the inhibitor binding was performed. The crystal structures of L492A mutant in a complex with CPPU and N-(2-chloro-pyridin-4-yl)-N -benzylurea (CPBU) were solved and confirm the importance of a stacking interaction between the 2-chloro-4-pyridinyl ring of the inhibitor and the isoalloxazine ring of the FAD cofactor. Amino derivatives like N-(2-amino-pyridin-4-yl)-N -phenylurea (APPU) inhibited ZmCKO1 more efficiently than CPPU, as opposed to the inhibition of E381A/S mutants, emphasizing the importance of this residue for inhibitor binding. As highly specific CKO inhibitors without undesired side effects are of major interest for physiological studies, all studied compounds were further analyzed for cytokinin activity in the Amaranthus bioassay and for binding to the Arabidopsis cytokinin receptors AHK3 and AHK4. By contrast to CPPU itself, APPU and several benzylureas bind only negligibly to the receptors and exhibit weak cytokinin activity.