Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyL, D-transpeptidase catalytic domain-like 8023139 4002015 SCOP2 (2022-06-29)
ASCOP2 FamilyL, D-transpeptidase pre-catalytic domain-like 8023141 4000465 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyL, D-transpeptidase catalytic domain-like 8035519 3000695 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyL, D-transpeptidase pre-catalytic domain-like 8035521 3000360 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AYkuDe1zatA1 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)
APG_binding_4e1zatA2 A: a+b complex topologyX: L,D-transpeptidase pre-catalytic domain-like (From Topology)H: L,D-transpeptidase pre-catalytic domain-like (From Topology)T: L,D-transpeptidase pre-catalytic domain-likeF: PG_binding_4ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.10.20.800 Alpha Beta Roll Ubiquitin-like (UB roll) CATH (4.3.0)
A2.40.440.10 Mainly Beta Beta Barrel L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-likeCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
PF12229Putative peptidoglycan binding domain (PG_binding_4)Putative peptidoglycan binding domainThis domain is found associated with the L,D-transpeptidase domain Pfam:PF03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be ...This domain is found associated with the L,D-transpeptidase domain Pfam:PF03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain (Bateman A pers. observation).
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
L,D-transpeptidase