2Y28

crystal structure of Se-Met AmpD derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and an Unprecedented Activation Mechanism.

Carrasco-Lopez, C.Rojas-Altuve, A.Zhang, W.Hesek, D.Lee, M.Barbe, S.Andre, I.Ferrer, P.Silva-Martin, N.Castro, G.R.Martinez-Ripoll, M.Mobashery, S.Hermoso, J.A.

(2011) J.Biol.Chem. 286: 31714

  • DOI: 10.1074/jbc.M111.264366
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of β-lactamase, a key enzyme of β-lactam antibiotic resistance. AmpD belongs to the amidase_2 family that includes zinc-dependent amidases and ...

    AmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of β-lactamase, a key enzyme of β-lactam antibiotic resistance. AmpD belongs to the amidase_2 family that includes zinc-dependent amidases and the peptidoglycan-recognition proteins (PGRPs), highly conserved pattern-recognition molecules of the immune system. Crystal structures of Citrobacter freundii AmpD were solved in this study for the apoenzyme, for the holoenzyme at two different pH values, and for the complex with the reaction products, providing insights into the PG recognition and the catalytic process. These structures are significantly different compared with the previously reported NMR structure for the same protein. The NMR structure does not possess an accessible active site and shows the protein in what is proposed herein as an inactive "closed" conformation. The transition of the protein from this inactive conformation to the active "open" conformation, as seen in the x-ray structures, was studied by targeted molecular dynamics simulations, which revealed large conformational rearrangements (as much as 17 Å) in four specific regions representing one-third of the entire protein. It is proposed that the large conformational change that would take the inactive NMR structure to the active x-ray structure represents an unprecedented mechanism for activation of AmpD. Analysis is presented to argue that this activation mechanism might be representative of a regulatory process for other intracellular members of the bacterial amidase_2 family of enzymes.


    Organizational Affiliation

    Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
A, B, C
187Citrobacter freundiiMutation(s): 0 
Gene Names: ampD
EC: 3.5.1.28
Find proteins for P82974 (Citrobacter freundii)
Go to UniProtKB:  P82974
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.178 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 67.693α = 90.00
b = 67.693β = 90.00
c = 92.681γ = 120.00
Software Package:
Software NamePurpose
SHELXphasing
XDSdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2011-09-14
    Type: Database references
  • Version 1.2: 2011-12-28
    Type: Other