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PDBsum entry 3d2y

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protein ligands links
Hydrolase PDB id
3d2y
Jmol
Contents
Protein chain
257 a.a. *
Ligands
AH0-ALA-FGA-LYS
GOL ×2
Waters ×308
* Residue conservation analysis
PDB id:
3d2y
Name: Hydrolase
Title: Complex of the n-acetylmuramyl-l-alanine amidase amid from e the substrate anhydro-n-acetylmuramic acid-l-ala-d-gamma-gl
Structure: N-acetylmuramoyl-l-alanine amidase amid. Chain: a. Engineered: yes. Anhydro-n-acetylmuramic acid-l-ala-d-gamma-glu-l- chain: b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 511145. Strain: k-12 mg1655. Gene: amid, ybjr, b0867, jw0851. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized
Resolution:
1.75Å     R-factor:   0.209     R-free:   0.253
Authors: F.Kerff,S.Petrella,R.Herman,E.Sauvage,F.Mercier,A.Luxen,J.M. B.Joris,P.Charlier
Key ref: F.Kerff et al. (2010). Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family. J Mol Biol, 397, 249-259. PubMed id: 20036252 DOI: 10.1016/j.jmb.2009.12.038
Date:
09-May-08     Release date:   16-Jun-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P75820  (AMID_ECOLI) -  N-acetylmuramoyl-L-alanine amidase AmiD
Seq:
Struc:
276 a.a.
257 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.28  - N-acetylmuramoyl-L-alanine amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     cell wall organization   2 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1016/j.jmb.2009.12.038 J Mol Biol 397:249-259 (2010)
PubMed id: 20036252  
 
 
Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family.
F.Kerff, S.Petrella, F.Mercier, E.Sauvage, R.Herman, A.Pennartz, A.Zervosen, A.Luxen, J.M.Frère, B.Joris, P.Charlier.
 
  ABSTRACT  
 
AmiD is the fifth identified N-acetylmuramoyl-L-alanine zinc amidase of Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane and has a broad specificity. AmiD is capable of cleaving the intact peptidoglycan (PG) as well as soluble fragments containing N-acetylmuramic acid regardless of the presence of an anhydro form or not, unlike the four other amidases, AmiA, AmiB, AmiC, and AmpD, which have some specificity. AmiD function is, however, not clearly established but it could be part of the enzymatic machinery involved in the PG turnover in E. coli. We solved three structures of the E. coli zinc amidase AmiD devoid of its lipidic anchorage: the holoenzyme, the apoenzyme in complex with the substrate anhydro-N-acetylmuramic-acid-L-Ala-gamma-d-Glu-L-Lys, and the holoenzyme in complex with the L-Ala-gamma-D-Glu-L-Lys peptide, the product of the hydrolysis of this substrate by AmiD. The AmiD structure shows a relatively flexible N-terminal extension that allows an easy reach of the PG by the enzyme inserted into the outer membrane. The C-terminal domain provides a potential extended geometrical complementarity to the substrate. AmiD shares a common fold with AmpD, the bacteriophage T7 lysozyme, and the PG recognition proteins, which are receptor proteins involved in the innate immune responses of a wide range of organisms. Analysis of the different structures reveals the similarity between the catalytic mechanism of zinc amidases of the AmiD family and the thermolysin-related zinc peptidases.