1R0M
Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Enolase N-terminal domain-like | 8044116 | 3001064 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Enolase C-terminal domain-like | 8044114 | 3000476 | 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 | SCOP2B Superfamily | Enolase N-terminal domain-like | 8044116 | 3001064 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Enolase C-terminal domain-like | 8044114 | 3000476 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Enolase C-terminal domain-like | 8044114 | 3000476 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Enolase N-terminal domain-like | 8044116 | 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) |
---|---|---|---|---|---|---|---|---|
A | MR_MLE_N | e1r0mA1 | 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: MR_MLE_N | ECOD (1.6) |
A | MR_MLE_C_1 | e1r0mA2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: MR_MLE_C_1 | ECOD (1.6) |
B | MR_MLE_N | e1r0mB1 | 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: MR_MLE_N | ECOD (1.6) |
B | MR_MLE_C_1 | e1r0mB2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: MR_MLE_C_1 | ECOD (1.6) |
C | MR_MLE_N | e1r0mC1 | 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: MR_MLE_N | ECOD (1.6) |
C | MR_MLE_C_1 | e1r0mC2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: MR_MLE_C_1 | ECOD (1.6) |
D | MR_MLE_N | e1r0mD1 | 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: MR_MLE_N | ECOD (1.6) |
D | MR_MLE_C_1 | e1r0mD2 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: MR_MLE_C_1 | 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 |
---|---|---|---|---|---|
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 | |
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 |
---|---|---|---|---|
N-acylamino acid racemase | - |
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR029065 | Enolase C-terminal domain-like | Domain | |
IPR013341 | Mandelate racemase/muconate lactonizing enzyme, N-terminal domain | Domain | |
IPR013342 | Mandelate racemase/muconate lactonizing enzyme, C-terminal | Domain | |
IPR029017 | Enolase-like, N-terminal | Homologous Superfamily | |
IPR010197 | o-Succinylbenzoate synthase/NAAAR | Family | |
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 |
---|---|---|---|
N-succinylamino acid racemase M-CSA #377 | N-succinylamino acid racemase (NAAAR) catalyses the racemisation of N-succinyl-D/L-amino acids, as part of a pathway for the conversion of D- to L-amino acids. NAAARs act on a broad range of N-acylamino acids rather than amino acids. This function is of significant interest in industry where enantiopure amino acids are inportant as chiral building blocks for antibiotics, herbicides, and drugs. The experimentally characterised enzyme from Geobacillus kaustophilus efficiently catalyses the racemisation of hydrophobic, polar, and some basic N-succinyl-D/L-amino acids. These enzymes are members of the enolase superfamily and highly similar to enzymes in the o-succinylbenzoate synthase family, and some may also function biologically as OSBSs. Although the reaction catalyzed by this family is similar to that catalyzed by the NSAR2 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 8 residues: SER:A-142LYS:A-168LYS:A-170ASP:A-195GLU:A-220ASP:A-245LYS:A-269GLY:A-297 | EC: 5.1.1 (UniProt) EC: 4.2.1.113 (UniProt) |