4BOL

Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with pentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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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:  
    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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AMPDH2A, B259Pseudomonas aeruginosa PAO1Mutation(s): 1 
Gene Names: ampDh2PA5485
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J0J (Subject of Investigation/LOI)
Query on J0J

Download Ideal Coordinates CCD File 
C [auth A], F [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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