1W1O

Native Cytokinin Dehydrogenase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1w1oa1	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	Cytokinin dehydrogenase 1	Cytokinin dehydrogenase 1	MAIZE (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
A	d1w1oa2	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	Cytokinin dehydrogenase 1	MAIZE (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cytokinin dehydrogenase 1	8029204	4002687	SCOP2 (2022-06-29)
A	SCOP2 Family	FAD-linked oxidases, N-terminal domain	8029206	4002178	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FAD-linked oxidases C-terminal domain-like	8041583	3001317	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FAD-binding/transporter-associated domain-like	8041585	3000913	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cytokin-bind	e1w1oA1	A: a+b two layers	X: Alpha-beta plaits	H: FAD-linked oxidases, C-terminal domain (From Topology)	T: FAD-linked oxidases, C-terminal domain	F: Cytokin-bind	ECOD (1.6)
A	FAD_binding_4	e1w1oA2	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
A	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
A	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09265	Cytokinin dehydrogenase 1, FAD and cytokinin binding (Cytokin-bind)	Cytokinin dehydrogenase 1, FAD and cytokinin binding	Members of this family adopt an alpha+beta sandwich structure with an antiparallel beta-sheet, in a ferredoxin-like fold. They are predominantly found in plant cytokinin dehydrogenase 1, where they are capable of binding both FAD and cytokinin substr ...	Members of this family adopt an alpha+beta sandwich structure with an antiparallel beta-sheet, in a ferredoxin-like fold. They are predominantly found in plant cytokinin dehydrogenase 1, where they are capable of binding both FAD and cytokinin substrates. 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 [1].	Domain
A	PF01565	FAD binding domain (FAD_binding_4)	FAD binding domain	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, call ...	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CYTOKININ DEHYDROGENASE 1	oxidoreductase activity catalytic activity oxidoreductase activity, acting on the CH-NH group of donors cytokinin dehydrogenase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	amine metabolic process cytokinin metabolic process regulation of hormone levels biological regulation metabolic process cellular process regulation of biological quality hormone metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A	IPR016164	FAD-linked oxidase-like, C-terminal	Homologous Superfamily
A	IPR016170	Cytokinin dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
A	IPR006094	FAD linked oxidase, N-terminal	Domain
A	IPR050432	FAD-linked Oxidoreductases in Biosynthesis Pathways	Family
A	IPR015345	Cytokinin dehydrogenase 1, FAD/cytokinin binding domain	Domain
A	IPR016166	FAD-binding domain, PCMH-type	Domain
A	IPR006093	Oxygen oxidoreductase covalent FAD-binding site	Binding Site
A	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	cytokinin dehydrogenase M-CSA #115	Cytokinin dehydrogenase (CKX) from Zea mays catalyses the irreversible oxidation of cytokinins, a type of plant hormone which promotes cell division and differentiation. CKX catalyses the conversion of N6-(delta2-isopentenyl)-adenine into adenine. Increased enzyme activity causes drastic abnormalities in the growth and development of the plant.	Defined by 3 residues: HIS:A-105ASP:A-169GLU:A-288 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.5.99.12 (PDB Primary Data) Search M-CSA Motif + EC 1.5.99.12

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.