2P8B

Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579 complexed with N-succinyl 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
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)
A	d2p8ba2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Bacillus cereus ATCC 14579 ) [TaxId: 226900 ],	SCOPe (2.08)
A	d2p8ba1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Bacillus cereus ATCC 14579 ) [TaxId: 226900 ],	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	e2p8bA1	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	e2p8bA2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	Mandelate racemase/muconate lactonizing enzyme family protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isomerase activity racemase and epimerase activity catalytic activity racemase activity, acting on amino acids and derivatives racemase and epimerase activity, acting on amino acids and derivatives	organic substance metabolic process metabolic process peptide metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029065	Enolase C-terminal domain-like	Domain
A	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain	Domain
A	IPR034603	Dipeptide epimerase	Family
A	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal	Domain
A	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
A	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	N-succinylamino acid racemase (type 2) M-CSA #958	Enzymes in the N-succinylamino acid racemase 2 (NSAR2) family catalyse the racemisation of N-succinyl arginine/lysine. Enzymes in this family are highly similar to enzymes in the dipeptide epimerase family. The experimentally characterised enzyme from Bacillus cereus has been shown to catalyse the epimerisation of certain dipeptides, but at a substantially lower rate than the racemisation of N-succinyl arginine/lysine. Although the reaction catalysed by this family is similar to that catalysed by the NSAR family (differing only in the preference of N-succinyl arginine/lysine for NSAR2 versus N-succinyl hydrophobic amino acids for NSAR), phylogenetic analysis suggests that these two families have independent evolutionary origins within the enolase superfamily. Not surprisingly, the amino acids responsible for substrate recognition appear to differ between the two families.	Defined by 5 residues: LYS:A-163ASP:A-191GLU:A-218ASP:A-243LYS:A-267 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif

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.