3P9I | pdb_00003p9i

Crystal structure of perennial ryegrass LpOMT1 complexed with S-adenosyl-L-homocysteine and sinapaldehyde

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3p9ia1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)
A	d3p9ia2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)
B	d3p9ib1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)
B	d3p9ib2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)
D	d3p9id1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)
D	d3p9id2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)
C	d3p9ic1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)
C	d3p9ic2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	perennial ryegrass (Lolium perenne ) [TaxId: 4522 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093275	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8093274	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093275	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8093274	3000034	SCOP2B (2022-06-29)
D	SCOP2 Family	Plant O-methyltransferase-like	8081399	4000240	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093275	3000118	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Winged helix DNA-binding domain	8093274	3000034	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8093274	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093275	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	e3p9iA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation	ECOD (1.6)
A	Methyltransf_11_4	e3p9iA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
B	Dimerisation	e3p9iB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation	ECOD (1.6)
B	Methyltransf_11_4	e3p9iB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
D	Dimerisation	e3p9iD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation	ECOD (1.6)
D	Methyltransf_11_4	e3p9iD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
C	Dimerisation	e3p9iC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation	ECOD (1.6)
C	Methyltransf_11_4	e3p9iC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	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	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	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	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)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
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)
C	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, C, D	PF08100	Plant O-methyltransferase dimerisation domain (Dimerisation)	Plant O-methyltransferase dimerisation domain	This domain is found at the N-terminus of plant O-methyltransferases involved in phenylpropanoid metabolism, including caffeic acid O-methyltransferase (COMT), isoflavone O-methyltransferase (IOMT), and chalcone O-methyltransferase (ChOMT). It media ...	This domain is found at the N-terminus of plant O-methyltransferases involved in phenylpropanoid metabolism, including caffeic acid O-methyltransferase (COMT), isoflavone O-methyltransferase (IOMT), and chalcone O-methyltransferase (ChOMT). It mediates dimerisation of these enzymes, which is critical for their activity [1-4]. The dimerisation domain forms the central core of the homodimer, with the SAM-binding domains located peripherally [1,3,4]. Dimerisation buries ~30% of the total surface area of the dimer [3]. The domain also contributes to forming the back wall of the substrate binding cavity of the partner monomer [2-4]. Structurally, the dimerisation domain consists primarily of alpha-helices [1-4]. Crystal structures reveal the domain is relatively rigid compared to the more mobile SAM-binding domain, which undergoes conformational changes upon substrate binding [4].	Domain
A, B, C, D	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, C, D	Caffeic acid O-methyltransferase	O-methyltransferase activity transferase activity, transferring one-carbon groups catechol O-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity protein binding binding protein dimerization activity	methylation metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

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