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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad6iywa1 All beta proteins Immunoglobulin-like beta-sandwich E set domains automated matches automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Ad6iywa2 All beta proteins L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Bd6iywb1 All beta proteins Immunoglobulin-like beta-sandwich E set domains automated matches automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Bd6iywb2 All beta proteins L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Cd6iywc1 All beta proteins Immunoglobulin-like beta-sandwich E set domains automated matches automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Cd6iywc2 All beta proteins L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Dd6iywd1 All beta proteins Immunoglobulin-like beta-sandwich E set domains automated matches automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Dd6iywd2 All beta proteins L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Ed6iywe1 All beta proteins Immunoglobulin-like beta-sandwich E set domains automated matches automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Ed6iywe2 All beta proteins L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Fd6iywf1 All beta proteins Immunoglobulin-like beta-sandwich E set domains automated matches automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Fd6iywf2 All beta proteins L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like automated matches (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ALDT_IgD_like_2e6iywA2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: LDT_IgD_like_2ECOD (1.6)
AYkuDe6iywA1 A: beta complex topologyX: L,D-transpeptidase catalytic domain-like (From Topology)H: L,D-transpeptidase catalytic domain-like (From Topology)T: L,D-transpeptidase catalytic domain-likeF: YkuDECOD (1.6)
BLDT_IgD_like_2e6iywB2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: LDT_IgD_like_2ECOD (1.6)
BYkuDe6iywB1 A: beta complex topologyX: L,D-transpeptidase catalytic domain-like (From Topology)H: L,D-transpeptidase catalytic domain-like (From Topology)T: L,D-transpeptidase catalytic domain-likeF: YkuDECOD (1.6)
CLDT_IgD_like_2e6iywC2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: LDT_IgD_like_2ECOD (1.6)
CYkuDe6iywC1 A: beta complex topologyX: L,D-transpeptidase catalytic domain-like (From Topology)H: L,D-transpeptidase catalytic domain-like (From Topology)T: L,D-transpeptidase catalytic domain-likeF: YkuDECOD (1.6)
DLDT_IgD_like_2e6iywD2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: LDT_IgD_like_2ECOD (1.6)
DYkuDe6iywD1 A: beta complex topologyX: L,D-transpeptidase catalytic domain-like (From Topology)H: L,D-transpeptidase catalytic domain-like (From Topology)T: L,D-transpeptidase catalytic domain-likeF: YkuDECOD (1.6)
ELDT_IgD_like_2e6iywE2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: LDT_IgD_like_2ECOD (1.6)
EYkuDe6iywE1 A: beta complex topologyX: L,D-transpeptidase catalytic domain-like (From Topology)H: L,D-transpeptidase catalytic domain-like (From Topology)T: L,D-transpeptidase catalytic domain-likeF: YkuDECOD (1.6)
FLDT_IgD_like_2e6iywF1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: LDT_IgD_like_2ECOD (1.6)
FYkuDe6iywF2 A: beta complex topologyX: L,D-transpeptidase catalytic domain-like (From Topology)H: L,D-transpeptidase catalytic domain-like (From Topology)T: L,D-transpeptidase catalytic domain-likeF: YkuDECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF03734L,D-transpeptidase catalytic domain (YkuD)L,D-transpeptidase catalytic domainThis 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 ...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-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
L,D-transpeptidase 2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR050979Bacterial L,D-transpeptidaseFamily
A, B, C, D, E
IPR041280Bacterial Ig domain, transpeptidase-associatedDomain
A, B, C, D, E
IPR005490L,D-transpeptidase catalytic domainDomain
A, B, C, D, E
IPR038063L,D-transpeptidase catalytic domain-likeHomologous Superfamily