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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family.

Kerff, F.Petrella, S.Mercier, F.Sauvage, E.Herman, R.Pennartz, A.Zervosen, A.Luxen, A.Frere, J.M.Joris, B.Charlier, P.

(2010) J.Mol.Biol. 397: 249-259

  • DOI: 10.1016/j.jmb.2009.12.038
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Centre d'Ingénierie des Protéines, University of Liège, Allée du 6 Août 17, Bât B5a, 4000 Liège, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylmuramoyl-L-alanine amidase amiD
A
261Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: amiD (ybjR)
EC: 3.5.1.28
Find proteins for P75820 (Escherichia coli (strain K12))
Go to UniProtKB:  P75820
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
B
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
AH0
Query on AH0
B
NON-POLYMERC11 H17 N O7

--

FGA
Query on FGA
B
D-gamma-peptide, C-delta linkingC5 H9 N O4

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.274α = 90.00
b = 88.274β = 90.00
c = 181.834γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
AMoREphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Advisory, Database references, Derived calculations, Non-polymer description