1XPY

Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans

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	d1xpya1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
A	d1xpya2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B	d1xpyb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B	d1xpyb2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C	d1xpyc1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C	d1xpyc2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
D	d1xpyd1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
D	d1xpyd2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	N-acylamino acid racemase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Enolase C-terminal domain-like	8044114	3000476	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase N-terminal domain-like	8044116	3001064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase C-terminal domain-like	8044114	3000476	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase N-terminal domain-like	8044116	3001064	SCOP2B (2022-06-29)
C	SCOP2 Family	D-glucarate dehydratase-like	8031736	4003246	SCOP2 (2022-06-29)
C	SCOP2 Family	Enolase N-terminal domain-like	8031738	4001209	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Enolase C-terminal domain-like	8044114	3000476	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Enolase N-terminal domain-like	8044116	3001064	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Enolase N-terminal domain-like	8044116	3001064	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase C-terminal domain-like	8044114	3000476	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	PF02746	e1xpyA1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
A	PF13378	e1xpyA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
B	PF02746	e1xpyB1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
B	PF13378	e1xpyB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
C	PF02746	e1xpyC1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
C	PF13378	e1xpyC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
D	PF02746	e1xpyD1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: PF02746	ECOD (1.6)
D	PF13378	e1xpyD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
B	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
C	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
D	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
D	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02746	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain (MR_MLE_N)	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain	SCOP reports fold similarity with enolase N-terminal domain.	Domain
A, B, C, D	PF13378	Enolase C-terminal domain-like (MR_MLE_C)	Enolase C-terminal domain-like	This domain appears at the C-terminus of many of the proteins that carry the MR_MLE_N Pfam:PF02746 domain. EC:4.2.1.40.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	N-acylamino acid racemase	isomerase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity O-succinylbenzoate synthase activity carbon-oxygen lyase activity	small molecule biosynthetic process cellular biosynthetic process cellular metabolic process cellular ketone metabolic process organic substance metabolic process biosynthetic process menaquinone metabolic process organic substance biosynthetic process small molecule metabolic process metabolic process cellular process menaquinone biosynthetic process ketone biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029065	Enolase C-terminal domain-like	Domain
A, B, C, D	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain	Domain
A, B, C, D	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal	Domain
A, B, C, D	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
A, B, C, D	IPR010197	o-Succinylbenzoate synthase/NAAAR	Family
A, B, C, D	IPR036849	Enolase-like, C-terminal 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.