Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with pentapeptide

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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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: https://doi.org/10.1021/ja405464b
  • Primary Citation of Related Structures:  
    4BJ4, 4BOL, 4BPA

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
259Pseudomonas aeruginosa PAO1Mutation(s): 1 
Find proteins for Q9HT86 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HT86 
Go to UniProtKB:  Q9HT86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HT86
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.63α = 90
b = 97.234β = 90
c = 104.169γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

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