4ML8 | pdb_00004ml8

Structure of maize cytokinin oxidase/dehydrogenase 2 (ZmCKO2)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4ml8d2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
D	d4ml8d1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
C	d4ml8c2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
C	d4ml8c1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
B	d4ml8b2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
B	d4ml8b1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
A	d4ml8a2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
A	d4ml8a1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	automated matches	automated matches	maize (Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Cytokin-bind	e4ml8D1	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)
D	FAD_binding_4	e4ml8D2	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)
C	Cytokin-bind	e4ml8C1	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)
C	FAD_binding_4	e4ml8C2	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)
B	Cytokin-bind	e4ml8B1	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)
B	FAD_binding_4	e4ml8B2	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)
A	Cytokin-bind	e4ml8A1	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	e4ml8A2	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)
D	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
D	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
D	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
C	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
C	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
C	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
B	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
B	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
B	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
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, B, C, D	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, B, C, D	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, B, C, D	Cytokinin oxidase 2	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 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	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.