Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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Ami_2

SMART accession number:	SM00644
Description:
Interpro abstract (IPR002502):	Proteins families 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 structure is known for the Bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.
GO process:	peptidoglycan catabolic process (GO:0009253)
GO function:	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 2419 Ami_2 domains in 2395 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a Ami_2 domain in a specific node, click on it.

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

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus

• 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
  2bgx		Crystal structure of native amid at 1.8 angstrom
  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)
  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)
  2z9n		Crystal structure of cameline peptidoglycan recognition protein at 3.2 a resolution
  3c2x		Crystal structure of peptidoglycan recognition protein at 1.8a resolution
  3c93		Crystal structure of the complex of peptidoglycan recognition protein (pgrp-s) with n-acetyl glucosamine (nag) at 2.6 a 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

• Links (links to other resources describing this domain)

• PFAM	Amidase_2
  INTERPRO	IPR002502

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