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	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)
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	Dimerisation	e1kywA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation	ECOD (1.6)
A	Methyltransf_11_2	e1kywA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
B [auth C]	Dimerisation	e1kywC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation	ECOD (1.6)
B [auth C]	Methyltransf_11_2	e1kywC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
C [auth F]	Dimerisation	e1kywF1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation	ECOD (1.6)
C [auth F]	Methyltransf_11_2	e1kywF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	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 cellular process phenylpropanoid metabolic process secondary metabolite biosynthetic process biosynthetic process phenylpropanoid biosynthetic process lignin biosynthetic process lignin metabolic process secondary metabolic 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 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.