PDBsum entry 3s1c

Oxidoreductase

PDB id: 3s1c

Contents

Protein chain

498 a.a.

Ligands

NAG-NAG

FAD

ZIR

GOL ×14

15P ×4

PEG ×4

NAG ×2

Waters ×324

PDB id:

3s1c

Name:

Oxidoreductase

Title:

Maize cytokinin oxidase/dehydrogenase complexed with n6- isopentenyladenosine

Structure:

Cytokinin dehydrogenase 1. Chain: a. Synonym: cytokinin oxidase 1, cko 1, cox 1, zmckx1. Engineered: yes

Source:

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

Resolution:

2.09Å R-factor: 0.215 R-free: 0.252

Authors:

D.Kopecny,P.Briozzo,S.Morera

Key ref:

D.Kopečný et al. (2016). Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site. Febs J, 283, 361-377. PubMed id: 26519657 DOI: 10.1111/febs.13581

Date:

15-May-11 Release date: 23-May-12

Protein chain

Q9T0N8  (CKX1_MAIZE) -  Cytokinin dehydrogenase 1 from Zea mays

Seq: 534 a.a.

Struc: 498 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 + A + H2O = 3-methyl-2-butenal + adenine + AH2

N(6)-dimethylallyladenine + + H2O (Bound ligand (Het Group name = ZIR) matches with 62.50% similarity) = 3-methyl-2-butenal + adenine + AH2

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1111/febs.13581

Febs J 283:361-377 (2016)

PubMed id: 26519657

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

D.Kopečný, R.Končitíková, H.Popelka, P.Briozzo, A.Vigouroux, M.Kopečná, D.Zalabák, M.Šebela, J.Skopalová, I.Frébort, S.Moréra.

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.