Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AYkuDe7ajxA1 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_1e7ajxA2 A: alpha arraysX: PGBD-like (From Topology)H: PGBD-like (From Topology)T: PGBD-likeF: PG_binding_1ECOD (1.6)
AF_UNCLASSIFIEDe7ajxA3 A: a+b complex topologyX: Lysozyme-like (From Homology)H: Lysozyme-likeT: Scaffolding domain of YcbBF: F_UNCLASSIFIEDECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF01471Putative peptidoglycan binding domain (PG_binding_1)Putative peptidoglycan binding domainThis domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is ...This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins [3]. The domain is found to bind peptidoglycan experimentally [4].
Domain
PF20142Scaffold domain (Scaffold)Scaffold domainThis entry represents the scaffolding domain from the L,D-transpeptidases [1].Domain
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
L,D-transpeptidase YcbB -