4BOL

Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with pentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reaction Products and the X-Ray Structure of Ampdh2, a Virulence Determinant of Pseudomonas Aeruginosa.

Martinez-Caballero, S.Lee, M.Artola-Recolons, C.Carrasco-Lopez, C.Hesek, D.Spink, E.E.Lastochkin, E.Zhang, W.Hellman, L.M.Boggess, B.Mobashery, S.Hermoso, J.A.

(2013) J.Am.Chem.Soc. 135: 10318

  • DOI: 10.1021/ja405464b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The zinc protease AmpDh2 is a virulence determinant of Pseudomonas aeruginosa, a problematic human pathogen. The mechanism of how the protease manifests virulence is not known, but it is known that it turns over the bacterial cell wall. The reaction ...

    The zinc protease AmpDh2 is a virulence determinant of Pseudomonas aeruginosa, a problematic human pathogen. The mechanism of how the protease manifests virulence is not known, but it is known that it turns over the bacterial cell wall. The reaction of AmpDh2 with the cell wall was investigated, and nine distinct turnover products were characterized by LC/MS/MS. The enzyme turns over both the cross-linked and noncross-linked cell wall. Three high-resolution X-ray structures, the apo enzyme and two complexes with turnover products, were solved. The X-ray structures show how the dimeric protein interacts with the inner leaflet of the bacterial outer membrane and that the two monomers provide a more expansive surface for recognition of the cell wall. This binding surface can accommodate the 3D solution structure of the cross-linked cell wall.


    Organizational Affiliation

    Department of Crystallography and Structural Biology, Inst. Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMPDH2
A, B
259Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutations: M17C
Gene Names: ampDh2
Find proteins for Q9HT86 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HT86
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
J0J
Query on J0J

Download SDF File 
Download CCD File 
A, B
D-alanyl-N-[(2S,6R)-6-amino-6-carboxy-1-{[(1R)-1-carboxyethyl]amino}-1-oxohexan-2-yl]-D-glutamine
C18 H31 N5 O9
VFGFFQOPKZHQLZ-PZWNZHSQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.630α = 90.00
b = 97.234β = 90.00
c = 104.169γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-07-24
    Type: Atomic model, Other
  • Version 1.2: 2013-07-31
    Type: Database references