1TKK | pdb_00001tkk

The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1tkkd1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1tkkd2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d1tkkh1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d1tkkh2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d1tkkg1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d1tkkg2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d1tkkf1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d1tkkf2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1tkke1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1tkke2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1tkkc1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1tkkc2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1tkkb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1tkkb2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1tkka1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1tkka2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	L-Ala-D/L-Glu epimerase	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase C-terminal domain-like	8037196	3000476	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase N-terminal domain-like	8037198	3001064	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	OsmC	e1tkkD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
D	Meth_synt_2	e1tkkD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
H	OsmC	e1tkkH1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
H	Meth_synt_2	e1tkkH2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
G	OsmC	e1tkkG1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
G	Meth_synt_2	e1tkkG2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
F	OsmC	e1tkkF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
F	Meth_synt_2	e1tkkF2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
E	OsmC	e1tkkE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
E	Meth_synt_2	e1tkkE2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
C	OsmC	e1tkkC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
C	Meth_synt_2	e1tkkC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
B	OsmC	e1tkkB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
B	Meth_synt_2	e1tkkB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
A	OsmC	e1tkkA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: OsmC	ECOD (v294.1)
A	Meth_synt_2	e1tkkA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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 A, B, C, D, E, F, G, H	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 A, B, C, D, E, F, G, H	similar to chloromuconate cycloisomerase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isomerase activity racemase and epimerase activity L-Ala-D/L-Glu epimerase activity racemase and epimerase activity, acting on amino acids and derivatives catalytic activity	metabolic process cellular process peptide metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization catabolic process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029065	Enolase_C-like	Unknown
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034603	Dipeptide epimerase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013342	Mandelate racemase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013341	Mandelate racemase, N-terminal domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	L-Ala-D/L-Glu epimerase M-CSA #957	L-Ala-D/L-Glu epimerase, first characterised from the bacteria Escherichia coli and Bacillus subtilis, catalyses the epimerisation of L-Ala-D-Glu to L-Ala-L-Glu and is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. In vitro the enzyme from Escherichia coli has been shown to epimerise several L-Ala-L-X dipeptides with broader specificity than the enzyme from Bacillus subtilis.	Defined by 5 residues: LYS:A-162ASP:A-191GLU:A-219ASP:A-244LYS:A-268 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.1.1.20 (UniProt) Search M-CSA Motif + EC 5.1.1.20

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.