3NYY

Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution

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	EUF08009	e3nyyA1	A: alpha arrays	X: N-terminal domain of lytM (From Topology)	H: N-terminal domain of lytM (From Topology)	T: N-terminal domain of lytM	F: EUF08009	ECOD (1.6)
A	Peptidase_M23	e3nyyA2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Duplicated hybrid motif	F: Peptidase_M23	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21640	LytM, N-terminal domain (LytM_N)	LytM, N-terminal domain	This domain is found at the N-terminal end of the peptidase from the M23 family LytM found in Ruminococcus gnavus and similar proteins predominantly found in firmicutes. This protein is predicted to have glycyl-glycine endopeptidase activity. This do ...	This domain is found at the N-terminal end of the peptidase from the M23 family LytM found in Ruminococcus gnavus and similar proteins predominantly found in firmicutes. This protein is predicted to have glycyl-glycine endopeptidase activity. This domain shows an all-alpha structure.	Domain
A	PF01551	Peptidase family M23 (Peptidase_M23)	Peptidase family M23	Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacte ...	Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putative glycyl-glycine endopeptidase lytM	peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR050570	Bacterial cell wall metabolism enzyme	Family
A	IPR016047	Peptidase M23	Domain
A	IPR048476	LytM, N-terminal domain	Domain
A	IPR011055	Duplicated hybrid motif	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.