4A52
NMR structure of the imipenem-acylated L,D-transpeptidase from Bacillus subtilis
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d4a52a2 | All beta proteins | L,D-transpeptidase catalytic domain-like | L,D-transpeptidase catalytic domain-like | L,D-transpeptidase catalytic domain-like | automated matches | (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], | SCOPe (2.08) |
A | d4a52a1 | Alpha and beta proteins (a+b) | LysM domain | LysM domain | automated matches | automated matches | (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], | SCOPe (2.08) |
A | d4a52a4 | Artifacts | Tags | Tags | Tags | C-terminal Tags | (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], | SCOPe (2.08) |
A | d4a52a3 | Artifacts | Tags | Tags | Tags | N-terminal Tags | (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | YkuD | e4a52A1 | A: beta complex topology | X: L,D-transpeptidase catalytic domain-like (From Topology) | H: L,D-transpeptidase catalytic domain-like (From Topology) | T: L,D-transpeptidase catalytic domain-like | F: YkuD | ECOD (1.6) |
A | LysM_1 | e4a52A2 | A: alpha arrays | X: HTH | H: LysM domain (From Topology) | T: LysM domain | F: LysM_1 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.10.350.10 | Alpha Beta | Roll | Membrane-bound Lytic Murein Transglycosylase D | Chain A | CATH (4.3.0) |
A | 2.40.440.10 | Mainly Beta | Beta Barrel | L,D-transpeptidase catalytic domain-like | L,D-transpeptidase catalytic domain-like | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF03734 | L,D-transpeptidase catalytic domain (YkuD) | L,D-transpeptidase catalytic domain | This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking [1]. This gives bacteria resistance to beta-lacta ... | Domain | |
PF01476 | LysM domain (LysM) | LysM domain | The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation [1]. This domain may have a general peptidoglycan binding function. The structure of this domain is known [2]. | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR050979 | Bacterial L,D-transpeptidase | Family | |
IPR036779 | LysM domain superfamily | Homologous Superfamily | |
IPR018392 | LysM domain | Domain | |
IPR005490 | L,D-transpeptidase catalytic domain | Domain | |
IPR038063 | L,D-transpeptidase catalytic domain-like | Homologous Superfamily |