1KDG

Crystal structure of the flavin domain of cellobiose 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	d1kdga1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), FAD-binding domain	(Phanerodontia chrysosporium ) [TaxId: 2822231 ],	SCOPe (2.08)
A	d1kdga2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GMC oxidoreductases	Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), substrate-binding domain	(Phanerodontia chrysosporium ) [TaxId: 2822231 ],	SCOPe (2.08)
B	d1kdgb1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), FAD-binding domain	(Phanerodontia chrysosporium ) [TaxId: 2822231 ],	SCOPe (2.08)
B	d1kdgb2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GMC oxidoreductases	Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), substrate-binding domain	(Phanerodontia chrysosporium ) [TaxId: 2822231 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GMC oxidoreductase-like	8001355	4000122	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoreductase-like	8055487	3000055	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Flavoreductase-like	8055487	3000055	SCOP2B (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	F_UNCLASSIFIED	e1kdgA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00732,PF00890,PF05199	e1kdgA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF00732,PF00890,PF05199	ECOD (1.6)
B	F_UNCLASSIFIED	e1kdgB1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00732,PF00890,PF05199	e1kdgB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF00732,PF00890,PF05199	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.410.10	Alpha Beta	2-Layer Sandwich	Cholesterol Oxidase	domain 2	CATH (4.3.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.30.410.10	Alpha Beta	2-Layer Sandwich	Cholesterol Oxidase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00732	GMC oxidoreductase (GMC_oxred_N)	GMC oxidoreductase	This family of proteins bind FAD as a cofactor.	Domain
A, B	PF05199	GMC oxidoreductase (GMC_oxred_C)	GMC oxidoreductase	This domain found associated with Pfam:PF00732.	Domain
A, B	PF13450	NAD(P)-binding Rossmann-like domain (NAD_binding_8)	NAD(P)-binding Rossmann-like domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	cellobiose dehydrogenase	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity oxidoreductase activity, acting on CH-OH group of donors cellobiose dehydrogenase (acceptor) activity cation binding ion binding binding metal ion binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity oxidoreductase activity, acting on CH-OH group of donors cellobiose dehydrogenase (acceptor) activity cation binding ion binding binding metal ion binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding	carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process organic substance metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellulose catabolic process carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process organic substance metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellulose catabolic process macromolecule metabolic process organic substance catabolic process cellulose metabolic process	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015920	Cellobiose dehydrogenase, cytochrome domain	Domain
A, B	IPR000172	Glucose-methanol-choline oxidoreductase, N-terminal	Domain
A, B	IPR005018	DOMON domain	Domain
A, B	IPR007867	Glucose-methanol-choline oxidoreductase, C-terminal	Domain
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	cellobiose dehydrogenase (acceptor) M-CSA #673	Fungal cellobiose dehydrogenase (CDH) participates in the rotting of wood by catalysing a key step in the breakdown of cellulose (and lignin), namely the oxidation of cellobiose (a reaction product in cellulose hydrolysis) to cellobiono-1,5-lactone. This is used to provide a carbon source for the micro-organism. CDH is the only known extracellular flavocytochrome, a small and heterogeneous group of redox-active proteins that carry both haem and flavin prosthetic groups. Applications of CDH include degradation of various environmental pollutants. It shows sequence and structural homology with glucose and cholesterol oxidase, two other known enzymes catalysing similar processes, so the mechanism is likely to be the same between the three. FAD is used as a cofactor for the reaction, being reduced by the substrate and subsequently reoxidised by a cytochromal haem group contained in the non-active site containing domain (PDB:1d7b)	Defined by 3 residues: TYR:A-400 [auth A-609]HIS:A-480 [auth A-689]ASN:A-523 [auth A-732] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.99.18 (PDB Primary Data) Search M-CSA Motif + EC 1.1.99.18

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.