2YII

Manipulating the regioselectivity of phenylalanine aminomutase: new insights into the reaction mechanism of MIO-dependent enzymes from structure-guided directed evolution

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	d2yiia_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	CHINESE YEW (Taxus chinensis ) [TaxId: 29808 ],	SCOPe (2.08)
B	d2yiib_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	CHINESE YEW (Taxus chinensis ) [TaxId: 29808 ],	SCOPe (2.08)
C	d2yiic_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	CHINESE YEW (Taxus chinensis ) [TaxId: 29808 ],	SCOPe (2.08)
D	d2yiid_	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	CHINESE YEW (Taxus chinensis ) [TaxId: 29808 ],	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	8076839	3001572	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L-aspartase-like	8076839	3001572	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartase-like	8076839	3001572	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L-aspartase-like	8076839	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	PF00221	e2yiiA2	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: PF00221	ECOD (1.6)
A	F_UNCLASSIFIED	e2yiiA1	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: F_UNCLASSIFIED	ECOD (1.6)
A	PF00221	e2yiiA3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: PF00221	ECOD (1.6)
B	PF00221	e2yiiB2	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: PF00221	ECOD (1.6)
B	F_UNCLASSIFIED	e2yiiB3	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: F_UNCLASSIFIED	ECOD (1.6)
B	PF00221	e2yiiB1	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: PF00221	ECOD (1.6)
C	PF00221	e2yiiC2	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: PF00221	ECOD (1.6)
C	F_UNCLASSIFIED	e2yiiC3	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: F_UNCLASSIFIED	ECOD (1.6)
C	PF00221	e2yiiC1	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: PF00221	ECOD (1.6)
D	PF00221	e2yiiD2	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: PF00221	ECOD (1.6)
D	F_UNCLASSIFIED	e2yiiD1	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: F_UNCLASSIFIED	ECOD (1.6)
D	PF00221	e2yiiD3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: PF00221	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 isomerase activity intramolecular aminotransferase activity intramolecular transferase activity	erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process organonitrogen compound metabolic process aromatic amino acid metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process L-phenylalanine metabolic process organic cyclic compound metabolic process proteinogenic amino acid metabolic process organic substance metabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process organonitrogen compound metabolic process aromatic amino acid metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process L-phenylalanine metabolic process organic cyclic compound metabolic process proteinogenic amino acid metabolic process organic substance metabolic process metabolic process small molecule metabolic process cellular process alkaloid biosynthetic process secondary metabolite biosynthetic process biosynthetic process organonitrogen compound biosynthetic process organic substance biosynthetic process alkaloid metabolic process secondary metabolic process catabolic process aromatic amino acid family catabolic process organic acid catabolic process cellular catabolic process carboxylic acid catabolic process amino acid catabolic process organonitrogen compound catabolic process L-phenylalanine catabolic process L-amino acid catabolic process organic cyclic compound catabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process organic substance catabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis diterpenoid metabolic process isoprenoid biosynthetic process cellular biosynthetic process lipid biosynthetic process terpenoid biosynthetic process diterpenoid biosynthetic process cellular lipid metabolic process paclitaxel biosynthetic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process cinnamic acid biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process cinnamic acid metabolic process phenylpropanoid metabolic process monocarboxylic acid biosynthetic process benzene-containing compound metabolic process small molecule biosynthetic process olefinic compound biosynthetic process phenylpropanoid biosynthetic process organic cyclic compound biosynthetic process olefinic compound metabolic process monocarboxylic acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

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	IPR008948	L-Aspartase-like	Homologous Superfamily
A, B, C, D	IPR031008	Phenylalanine aminomutase (L-beta-phenylalanine forming)	Family
A, B, C, D	IPR022313	Phenylalanine/histidine ammonia-lyases, active site	Active Site
A, B, C, D	IPR023144	Phenylalanine ammonia-lyase, shielding domain superfamily	Homologous Superfamily

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.