CRYSTAL STRUCTURE OF A D-AMINOPEPTIDASE FROM OCHROBACTRUM ANTHROPI
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
| Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
|---|---|---|---|---|---|---|---|---|
| A | d1ei5a1 | All beta proteins | Streptavidin-like | D-aminopeptidase, middle and C-terminal domains | D-aminopeptidase, middle and C-terminal domains | D-aminopeptidase, middle and C-terminal domains | (Brucella anthropi ) [TaxId: 529 ], | SCOPe (2.08) |
| A | d1ei5a3 | Multi-domain proteins (alpha and beta) | beta-lactamase/transpeptidase-like | beta-lactamase/transpeptidase-like | beta-Lactamase/D-ala carboxypeptidase | D-aminopeptidase, N-terminal domain | (Brucella anthropi ) [TaxId: 529 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| A | SCOP2 Family | beta-Lactamase/D-ala carboxypeptidase | 8024999 | 4002685 | SCOP2 (2022-06-29) |
| A | SCOP2 Family | D-aminopeptidase, middle and C-terminal domains | 8030361 | 4002614 | SCOP2 (2022-06-29) |
| A | SCOP2 Family | D-aminopeptidase, middle and C-terminal domains | 8030363 | 4002614 | SCOP2 (2022-06-29) |
| A | SCOP2 Superfamily | beta-lactamase/transpeptidase-like | 8037378 | 3001604 | SCOP2 (2022-06-29) |
| A | SCOP2 Superfamily | D-aminopeptidase associated domain-like | 8042740 | 3001485 | SCOP2 (2022-06-29) |
| A | SCOP2 Superfamily | D-aminopeptidase associated domain-like | 8042742 | 3001485 | SCOP2 (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 | DAP_B | e1ei5A1 | A: beta barrels | X: Lipocalins/Streptavidin | H: D-aminopeptidase, middle and C-terminal domains | T: D-aminopeptidase, middle and C-terminal domains | F: DAP_B | ECOD (v294.2) |
| A | Beta-lactamase | e1ei5A3 | A: a+b two layers | X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins | H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins | T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins | F: Beta-lactamase | ECOD (v294.2) |
| A | Transpeptidase | e1ei5A4 | A: a+b three layers | X: Profilin-like | H: a+b domain in beta-lactamase/transpeptidase-like proteins | T: a+b domain in beta-lactamase/transpeptidase-like proteins | F: Transpeptidase | ECOD (v294.2) |
Domain Annotation: CATH CATH Database Homepage
| Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
|---|---|---|---|---|---|---|
| A | 3.40.710.10 | Alpha Beta | 3-Layer(aba) Sandwich | Beta-lactamase | DD-peptidase/beta-lactamase superfamily | CATH (4.3.0) |
| A | 2.40.128.50 | Mainly Beta | Beta Barrel | Lipocalin | CATH (4.3.0) |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
| Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
|---|---|---|---|---|
| D-AMINOPEPTIDASE | - |
InterPro: Protein Family Classification InterPro Database Homepage
| Chains | Accession | Name | Type |
|---|---|---|---|
| IPR001466 | Beta-lactamase-related | Domain | |
| IPR012338 | Beta-lactamase/transpeptidase-like | Homologous Superfamily | |
| IPR012856 | D-aminopeptidase, domain B | Domain | |
| IPR050491 | Beta-lactamase AmpC-like | Family | |
| IPR023645 | D-aminopeptidase | Family | |
| IPR027279 | D-aminopeptidase/lipoprotein domain superfamily | Homologous Superfamily |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
| Chains | Enzyme Name | Description | Catalytic Residues |
|---|---|---|---|
| D-stereospecific aminopeptidase (peptidase S12 family) M-CSA #782 | Antibiotic resistance to the beta lactam family of antibiotics, which includes penicillin, is often conferred to bacteria by serine beta lactamases which can break down the inhibitor to harmless products. They are believed to have evolved from D amino peptidases, which hydrolyse the peptide bond between two D amino acids after the N terminal residue. DAP from Othrobacrum anthropi is one such peptidase, and is inhibited by beta lactams. Study of this protein will thus reveal details of how the antibiotic resistance conferring peptidases work. It is found to show significant active site homology with other penicillin binding proteins, including the serine beta lactamases, but very low sequence identity with either group, suggesting that it is part of a novel family which may have given rise to the resistance-conferring enzymes. | Defined by 5 residues: SER:A-62LYS:A-65TYR:A-153ASN:A-155HIS:A-287 | EC: 3.4.11.19 (PDB Primary Data) |














