Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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Ami_2

SMART accession number:	SM00644
Description:	-
Interpro abstract (IPR002502):	Proteins containing this domain include 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 bacteriophage endolysins PLY118 and PLY500 cleave between L-Ala and D-Glu residues of Listeria cell-wall peptidoglycan and are therefore peptidases (MEROPS subfamily M15C) [ (PUBMED:8577256) ]. The structure is known for the Bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding [ (PUBMED:14506276) (PUBMED:12845326) (PUBMED:8171031) (PUBMED:15223330) (PUBMED:16556841) (PUBMED:18304640) (PUBMED:15140887) (PUBMED:16103125) (PUBMED:16428381) ].
GO process:	peptidoglycan catabolic process (GO:0009253)
GO function:	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 27919 Ami_2 domains in 27615 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing Ami_2 domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Ami_2 domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing Ami_2 domain in the selected taxonomic class.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 80.58 map00550 Peptidoglycan biosynthesis 8.25 map00511 N-Glycan degradation 8.25 map01032 Glycan structures - degradation 0.49 map00380 Tryptophan metabolism 0.49 map00220 Urea cycle and metabolism of amino groups 0.49 map00643 Styrene degradation 0.49 map00460 Cyanoamino acid metabolism 0.49 map00360 Phenylalanine metabolism 0.49 map00632 Benzoate degradation via CoA ligation This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with Ami_2 domain which could be assigned to a KEGG orthologous group, and not all proteins containing Ami_2 domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of Ami_2 domains in PDB

  PDB code	Main view	Title
  1aro		T7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME
  1j3g		Solution structure of Citrobacter Freundii AmpD
  1lba		THE STRUCTURE OF BACTERIOPHAGE T7 LYSOZYME, A ZINC AMIDASE AND AN INHIBITOR OF T7 RNA POLYMERASE
  1oht		Peptidoglycan recognition protein LB
  1s2j		Crystal structure of the Drosophila pattern-recognition receptor PGRP-SA
  1sk3		Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha
  1sk4		crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha
  1sxr		Drosophila Peptidoglycan Recognition Protein (PGRP)-SA
  1twq		Crystal structure of the C-terminal PGN-binding domain of human PGRP-Ialpha in complex with PGN analog muramyl tripeptide
  1yb0		Structure of PlyL
  1yck		Crystal structure of human peptidoglycan recognition protein (PGRP-S)
  2aph		Crystal structure of human PGRP-IalphaC in complex with muramyl pentapeptide
  2ar3		E90A mutant structure of PlyL
  2bh7		Crystal structure of a SeMet derivative of AmiD at 2.2 angstroms
  2cb3		Crystal structure of peptidoglycan recognition protein-LE in complex with tracheal cytotoxin (monomeric diaminopimelic acid-type peptidoglycan)
  2eav		Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ibeta
  2eax		Crystal structure of human PGRP-IBETAC in complex with glycosamyl muramyl pentapeptide
  2f2l		Crystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of peptidoglycan recognition proteins LCa (PGRP-LCa) and LCx (PGRP-LCx)
  2l47		Solution structure of the PlyG catalytic domain
  2r2k		Crystal structure of the complex of camel peptidoglycan recognition protein with disaccharide at 3.2A resolution
  2r90		Crystal structure of cameline peptidoglycan recognition protein at 2.8A resolution
  2rkq		Crystal structure of drosophila peptidoglycan recognition protein SD (PGRP-SD)
  2wkx		Crystal structure of the native E. coli zinc amidase AmiD
  2xz4		Crystal structure of the LFZ ectodomain of the peptidoglycan recognition protein LF
  2y28		crystal structure of Se-Met AmpD derivative
  2y2b		crystal structure of AmpD in complex with reaction products
  2y2c		crystal structure of AmpD Apoenzyme
  2y2d		crystal structure of AmpD holoenzyme
  2y2e		crystal structure of AmpD grown at pH 5.5
  2z9n		Crystal structure of cameline peptidoglycan recognition protein at 3.2 A resolution
  3c2x		Crystal structure of peptidoglycan recognition protein at 1.8A resolution
  3cg9		Crystal structure of the complex of peptidoglycan recognition protein with methyloxane-2,3,4,5-tetrol at 2.9 A resolution
  3cor		Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with N-acetylgalactosamine at 3.1 A resolution
  3cxa		Crystal structure of the complex of peptidoglycan recognition protein with alpha-D-glucopyranosyl alpha-D-glucopyranoside at 3.4 A resolution
  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
  3d2z		Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the product L-Ala-D-gamma-Glu-L-Lys
  3hmb		Mutant endolysin from Bacillus subtilis
  3lat		Crystal structure of Staphylococcus peptidoglycan hydrolase AmiE
  3ng4		Ternary complex of peptidoglycan recognition protein (PGRP-S) with Maltose and N-Acetylglucosamine at 1.7 A Resolution
  3nno		Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with Alpha-Rhamnose at 2.9 A resolution
  3nw3		Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with the PGN Fragment at 2.5 A resolution
  3o4k		Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) and lipoteichoic acid at 2.1 A resolution
  3ogx		Crystal structure of the complex of Peptidoglycan Recognition protein (PGRP-s) with Heparin-Dissacharide at 2.8 A resolution
  3qj1		Crystal structure of camel peptidoglycan recognition protein, PGRP-S with a trapped diethylene glycol in the ligand diffusion channel at 3.2 A resolution
  3qs0		Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with a bound N-acetylglucosamine in the diffusion channel at 2.5 A resolution
  3qv4		Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with dipeptide L-ALA D-GLU at 2.7 A resolution
  3rdr		Structure of the catalytic domain of XlyA
  3rt4		Structural Basis of Recognition of Pathogen-associated Molecular Patterns and Inhibition of Proinflammatory Cytokines by Camel Peptidoglycan Recognition Protein
  3t2v		Crystal structure of the complex of peptidoglycan recognition protein-short (CPGRP-S) with mycolic acid at 2.5 A resolution
  3t39		Crystal structure of the complex of camel peptidoglycan recognition protein(CPGRP-S) with a mycobacterium metabolite shikimate at 2.7 A resolution
  3tru		Crystal structure of the complex of peptidoglycan recognition protein with cellular metabolite chorismate at 3.2 A resolution
  3uil		Crystal Structure of the complex of PGRP-S with lauric acid at 2.2 A resolution
  3uml		Crystal structure of PGRP-S complexed with chorismate at 2.15 A resolution
  3umq		Crystal structure of peptidoglycan recognition protein-S complexed with butyric acid at 2.2 A resolution
  3usx		Crystal structure of PGRP-S complexed with Myristic Acid at 2.28 A resolution
  4bj4		Structure of Pseudomonas aeruginosa amidase Ampdh2
  4bol		Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with pentapeptide
  4bpa		Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with NAG-NAM-NAG-NAM tetrasaccharide
  4bxd		CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TETRASACCHARIDE PENTAPEPTIDE
  4bxe		CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ANHYDROMURAMIC PENTAPEPTIDE
  4bxj		CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA
  4fnn		Crystal structure of the complex of CPGRP-S with stearic acid at 2.2 A RESOLUTION
  4gf9		Structural insights into the dual strategy of recognition of peptidoglycan recognition protein, PGRP-S: ternary complex of PGRP-S with LPS and fatty acid
  4ivv		Catalytic amidase domain of the major autolysin LytA from Streptococcus pneumaniae
  4knk		Crystal structure of Staphylococcus aureus hydrolase AmiA
  4knl		Crystal structure of Staphylococcus aureus hydrolase AmiA in complex with its ligand
  4ols		4OLS
  4opp		Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 11-cyclohexylundecanoic acid and N- acetylglucosamine at 2.30 A resolution
  4orv		Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution
  4oug		Crystal structure of the ternary complex of camel peptidoglycan recognition protein, PGRP-S with lipopolysaccharide and palmitic acid at 2.46 A resolution
  4q8s		Crystal structure of mammalian Peptidoglycan recognition protein PGRP-S with paranitrophenyl palmitate and N-acetyl glucosamine at 2.09 A resolution
  4q9e		Structure of the ternary complex of peptidoglycan recognition protein, PGRP-S with N-acetyl glucosamine and paranitro benzaldehyde at 2.3 A resolution
  4x36		4X36
  4z8i		4Z8I
  4zxm		4ZXM
  5ctv		5CTV
  5dwf		5DWF
  5e0a		5E0A
  5e0b		5E0B

• Links (links to other resources describing this domain)

• PFAM	Amidase_2
  INTERPRO	IPR002502

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