4PGH | pdb_00004pgh

Caffeic acid O-methyltransferase from Sorghum bicolor

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)
D	d4pghd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)
D	d4pghd2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)
C	d4pghc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)
C	d4pghc2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)
B	d4pghb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)
B	d4pghb2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)
A	d4pgha1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)
A	d4pgha2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Sorghum (Sorghum bicolor ) [TaxId: 4558 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	Plant O-methyltransferase-like	8081398	4000240	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093273	3000118	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Winged helix DNA-binding domain	8093272	3000034	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8093272	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093273	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093273	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8093272	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8093272	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8093273	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)
D	YajR_YAM	e4pghD1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
C	YajR_YAM	e4pghC1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
B	YajR_YAM	e4pghB1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)
A	YajR_YAM	e4pghA1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08100	O-methyltransferase dimerisation domain (Dimerisation)	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 mediat ...	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].ED A0A553NLB0.1/265-321; A0A553NLB0.1/265-293;	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	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity O-methyltransferase activity flavone 3'-O-methyltransferase activity acetylserotonin O-methyltransferase activity caffeate O-methyltransferase activity protein binding binding protein dimerization activity	regulation of hormone levels biological regulation indole-containing compound metabolic process hormone metabolic process melatonin metabolic process biosynthetic process indole-containing compound biosynthetic process metabolic process cellular process regulation of biological quality melatonin biosynthetic process hormone biosynthetic process methylation phenylpropanoid metabolic process regulation of hormone levels biological regulation indole-containing compound metabolic process hormone metabolic process melatonin metabolic process biosynthetic process indole-containing compound biosynthetic process metabolic process cellular process regulation of biological quality melatonin biosynthetic process hormone biosynthetic process methylation phenylpropanoid metabolic process secondary metabolite biosynthetic process phenylpropanoid biosynthetic process lignin biosynthetic process lignin metabolic process secondary metabolic process pigment metabolic process flavonoid metabolic process pigment biosynthetic process flavonol biosynthetic process flavonoid biosynthetic process flavonol metabolic process flavone biosynthetic process flavone metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR016461	O-methyltransferase-like	Family
A, B, C, D	IPR001077	O-methyltransferase, C-terminal domain	Domain
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR012967	Caffeic acid 3-O-methyltransferase-like, dimerisation domain	Domain
A, B, C, D	IPR022657	Orn/DAP/Arg decarboxylase 2, conserved site	Conserved Site

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.