3RIT

Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg and dipeptide L-Arg-D-Lys

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3rita2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
A	d3rita1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
B	d3ritb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
B	d3ritb1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
C	d3ritc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
C	d3ritc1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
D	d3ritd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
D	d3ritd1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
E	d3rite2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)
E	d3rite1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Methylococcus capsulatus ) [TaxId: 414 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF02746	e3ritA1	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	e3ritA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
B	PF02746	e3ritB1	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	e3ritB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
C	PF02746	e3ritC1	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	e3ritC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
D	PF02746	e3ritD1	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	e3ritD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
E	PF02746	e3ritE1	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)
E	PF13378	e3ritE2	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)
E	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
E	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, E	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, E	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, E	Dipeptide epimerase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding intramolecular lyase activity isomerase activity chloromuconate cycloisomerase activity catalytic activity racemase and epimerase activity racemase and epimerase activity, acting on amino acids and derivatives	organic substance metabolic process metabolic process peptide metabolic process catabolic process amino acid metabolic process primary metabolic process amino acid catabolic process organic substance catabolic process catechol-containing compound catabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process organic cyclic compound catabolic process phenol-containing compound catabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process peptide metabolic process catabolic process amino acid metabolic process primary metabolic process amino acid catabolic process organic substance catabolic process catechol-containing compound catabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process organic cyclic compound catabolic process phenol-containing compound catabolic process organic cyclic compound metabolic process organic hydroxy compound catabolic process phenol-containing compound metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain	Domain
A, B, C, D, E	IPR034603	Dipeptide epimerase	Family
A, B, C, D, E	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site	Conserved Site
A, B, C, D, E	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR029065	Enolase C-terminal domain-like	Domain
A, B, C, D, E	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal	Domain
A, B, C, D, E	IPR029017	Enolase-like, N-terminal	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.