3D2Y

Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the substrate anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8038051	3000555	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PGBD-like	8038048	3001357	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UNK_F_TYPE	e3d2yA1	A: alpha arrays	X: PGBD-like (From Topology)	H: PGBD-like (From Topology)	T: PGBD-like	F: UNK_F_TYPE	ECOD (1.6)
A	Amidase_2	e3d2yA2	A: a+b three layers	X: N-acetylmuramoyl-L-alanine amidase-like (From Topology)	H: N-acetylmuramoyl-L-alanine amidase-like (From Topology)	T: N-acetylmuramoyl-L-alanine amidase-like	F: Amidase_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)
A	1.10.101.10	Mainly Alpha	Orthogonal Bundle	Muramoyl-pentapeptide Carboxypeptidase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01510	N-acetylmuramoyl-L-alanine amidase (Amidase_2)	N-acetylmuramoyl-L-alanine amidase	This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The ...	This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	N-acetylmuramoyl-L-alanine amidase amiD	N-acetyl-anhydromuramoyl-L-alanine amidase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding peptidoglycan muralytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides N-acetylmuramoyl-L-alanine amidase activity	organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process organic substance metabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process organic substance metabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process macromolecule metabolic process organic substance catabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization peptidoglycan turnover	membrane outer membrane cellular anatomical entity cell periphery cell outer membrane external encapsulating structure cell envelope
B	Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036365	PGBD-like superfamily	Homologous Superfamily
A	IPR002502	N-acetylmuramoyl-L-alanine amidase domain	Domain
A	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily	Homologous Superfamily
A	IPR036366	PGBD superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.