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)

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

Metabolism (metabolic pathways involving proteins which contain this domain)

% 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	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