7AJO | pdb_00007ajo

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with the cross-linking reaction intermediate

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YkuD	e7ajoA1	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	PG_binding_1	e7ajoA3	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: PG_binding_1	ECOD (1.6)
A	F_UNCLASSIFIED	e7ajoA2	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Scaffolding domain of YcbB	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01471	Putative peptidoglycan binding domain (PG_binding_1)	Putative peptidoglycan binding domain	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 ...	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
A	PF20142	Scaffold domain (Scaffold)	Scaffold domain	This entry represents the scaffolding domain from the L,D-transpeptidases [1].	Domain
A	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 ...	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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	L,D-transpeptidase YcbB	peptidase activity catalytic activity, acting on a protein hydrolase activity exopeptidase activity catalytic activity carboxypeptidase activity transferase activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR052905	L,D-transpeptidase YkuD-like	Family
A	IPR002477	Peptidoglycan binding-like	Domain
A	IPR036365	PGBD-like superfamily	Homologous Superfamily
A	IPR045380	L,D-transpeptidase, scaffold domain	Domain
A	IPR036366	PGBD superfamily	Homologous Superfamily
A	IPR005490	L,D-transpeptidase catalytic domain	Domain
A	IPR038063	L,D-transpeptidase catalytic domain-like	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.