1Y2M

Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides

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	d1y2ma_	All alpha proteins	L-aspartase-like	L-aspartase-like	HAL/PAL-like	Phenylalanine ammonia-lyase, PAL	(Rhodotorula toruloides ) [TaxId: 5286 ],	SCOPe (2.08)
B	d1y2mb_	All alpha proteins	L-aspartase-like	L-aspartase-like	HAL/PAL-like	Phenylalanine ammonia-lyase, PAL	(Rhodotorula toruloides ) [TaxId: 5286 ],	SCOPe (2.08)
C	d1y2mc_	All alpha proteins	L-aspartase-like	L-aspartase-like	HAL/PAL-like	Phenylalanine ammonia-lyase, PAL	(Rhodotorula toruloides ) [TaxId: 5286 ],	SCOPe (2.08)
D	d1y2md_	All alpha proteins	L-aspartase-like	L-aspartase-like	HAL/PAL-like	Phenylalanine ammonia-lyase, PAL	(Rhodotorula toruloides ) [TaxId: 5286 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	L-aspartase-like	8042400	3001572	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L-aspartase-like	8042400	3001572	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartase-like	8042400	3001572	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L-aspartase-like	8042400	3001572	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	Lyase_aromatic_N	e1y2mA2	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Lyase_aromatic_N	ECOD (1.6)
A	phe_am_lyase	e1y2mA1	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: phe_am_lyase	ECOD (1.6)
A	Lyase_aromatic_C	e1y2mA3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_aromatic_C	ECOD (1.6)
B	Lyase_aromatic_N	e1y2mB4	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Lyase_aromatic_N	ECOD (1.6)
B	phe_am_lyase	e1y2mB5	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: phe_am_lyase	ECOD (1.6)
B	Lyase_aromatic_C	e1y2mB6	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_aromatic_C	ECOD (1.6)
C	Lyase_aromatic_N	e1y2mC2	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Lyase_aromatic_N	ECOD (1.6)
C	phe_am_lyase	e1y2mC1	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: phe_am_lyase	ECOD (1.6)
C	Lyase_aromatic_C	e1y2mC3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_aromatic_C	ECOD (1.6)
D	Lyase_aromatic_N	e1y2mD1	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Lyase_aromatic_N	ECOD (1.6)
D	phe_am_lyase	e1y2mD5	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: phe_am_lyase	ECOD (1.6)
D	Lyase_aromatic_C	e1y2mD3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_aromatic_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
A	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
A	1.10.274.20	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
B	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
B	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
B	1.10.274.20	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
C	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
C	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
C	1.10.274.20	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
D	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
D	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
D	1.10.274.20	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00221	Aromatic amino acid lyase (Lyase_aromatic)	Aromatic amino acid lyase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Phenylalanine ammonia-lyase	phenylalanine ammonia-lyase activity lyase activity ammonia-lyase activity catalytic activity carbon-nitrogen lyase activity tyrosine ammonia-lyase activity	catabolic process oxoacid metabolic process aromatic amino acid family catabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process L-phenylalanine catabolic process aromatic amino acid metabolic process catabolic process oxoacid metabolic process aromatic amino acid family catabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process L-phenylalanine catabolic process aromatic amino acid metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process L-phenylalanine metabolic process proteinogenic amino acid metabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process phenylpropanoid metabolic process cinnamic acid biosynthetic process monocarboxylic acid biosynthetic process benzene-containing compound metabolic process small molecule biosynthetic process olefinic compound biosynthetic process organic acid biosynthetic process phenylpropanoid biosynthetic process carboxylic acid biosynthetic process secondary metabolic process biosynthetic process secondary metabolite biosynthetic process olefinic compound metabolic process monocarboxylic acid metabolic process cinnamic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR005922	Phenylalanine ammonia-lyase	Family
A, B, C, D	IPR024083	Fumarase/histidase, N-terminal	Homologous Superfamily
A, B, C, D	IPR001106	Aromatic amino acid lyase	Family
A, B, C, D	IPR022313	Phenylalanine/histidine ammonia-lyases, active site	Active Site
A, B, C, D	IPR008948	L-Aspartase-like	Homologous Superfamily
A, B, C, D	IPR023144	Phenylalanine ammonia-lyase, shielding 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.