1KYW

Crystal Structure Analysis of Caffeic Acid/5-hydroxyferulic acid 3/5-O-methyltransferase in complex with 5-hydroxyconiferaldehyde

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	d1kywa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Plant O-methyltransferase, N-terminal domain	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase	(Medicago sativa ) [TaxId: 3879 ],	SCOPe (2.08)
A	d1kywa2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Plant O-methyltransferase, C-terminal domain	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase	(Medicago sativa ) [TaxId: 3879 ],	SCOPe (2.08)
B [auth C]	d1kywc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Plant O-methyltransferase, N-terminal domain	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase	(Medicago sativa ) [TaxId: 3879 ],	SCOPe (2.08)
B [auth C]	d1kywc2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Plant O-methyltransferase, C-terminal domain	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase	(Medicago sativa ) [TaxId: 3879 ],	SCOPe (2.08)
C [auth F]	d1kywf1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Plant O-methyltransferase, N-terminal domain	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase	(Medicago sativa ) [TaxId: 3879 ],	SCOPe (2.08)
C [auth F]	d1kywf2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Plant O-methyltransferase, C-terminal domain	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase	(Medicago sativa ) [TaxId: 3879 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8054287	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8054286	3000118	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8054287	3000034	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8054286	3000118	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	Winged helix DNA-binding domain	8054287	3000034	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8054286	3000118	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	PF08100	e1kywA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF08100	ECOD (1.6)
A	PF00891	e1kywA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF00891	ECOD (1.6)
B [auth C]	PF08100	e1kywC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF08100	ECOD (1.6)
B [auth C]	PF00891	e1kywC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF00891	ECOD (1.6)
C [auth F]	PF08100	e1kywF1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF08100	ECOD (1.6)
C [auth F]	PF00891	e1kywF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF00891	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B [auth C]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B [auth C]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C [auth F]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C [auth F]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth F]	PF08100	Dimerisation domain (Dimerisation)	Dimerisation domain	This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [1].	Domain
A, B [auth C], C [auth F]	PF00891	O-methyltransferase domain (Methyltransf_2)	O-methyltransferase domain	This family includes a range of O-methyltransferases. These enzymes utilise S-adenosyl methionine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth F]	Caffeic acid 3-O-methyltransferase	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity protein binding binding protein dimerization activity O-methyltransferase activity caffeate O-methyltransferase activity	methylation metabolic process phenylpropanoid metabolic process phenylpropanoid biosynthetic process lignin metabolic process secondary metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process secondary metabolite biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process lignin biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth F]	IPR001077	O-methyltransferase domain	Domain
A, B [auth C], C [auth F]	IPR016461	O-methyltransferase COMT-type	Family
A, B [auth C], C [auth F]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B [auth C], C [auth F]	IPR012967	Plant methyltransferase dimerisation domain	Domain
A, B [auth C], C [auth F]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B [auth C], C [auth F]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	caffeate O-methyltransferase M-CSA #621	COMT is involved in lignin biosynthesis - it methylates caffeoyl- and 5-hydroxyferuloyl-containing acids, aldehydes and alcohols. Lignin polymerisation has implications in industrial, environmental and agricultural areas.	Defined by 4 residues: HIS:A-269ASP:A-270GLU:A-297GLU:A-329 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.68 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.68

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.