Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.79 kDa 
• Atom Count: 4330 
• Modelled Residue Count: 509 
• Deposited Residue Count: 510 
• Unique protein chains: 1

4BXJ

CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA

• PDB DOI: 10.2210/pdb4BXJ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-07-12 Released: 2013-10-09 
• Deposition Author(s): Carrasco-Lopez, C., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Cell-Wall Remodeling by the Zinc-Protease Ampdh3 from Pseudomonas Aeruginosa.

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

(2013) J Am Chem Soc 135: 12604

• PubMed: 23931161 
• DOI: 10.1021/ja407445x
• Primary Citation of Related Structures:  
  4BXD, 4BXE, 4BXJ


• PubMed Abstract: 
  

Bacterial cell wall is a polymer of considerable complexity that is in constant equilibrium between synthesis and recycling. AmpDh3 is a periplasmic zinc protease of Pseudomonas aeruginosa , which is intimately involved in cell-wall remodeling. We document the hydrolytic reactions that this enzyme performs on the cell wall. The process removes the peptide stems from the peptidoglycan, the major constituent of the cell wall. We document that the majority of the reactions of this enzyme takes place on the polymeric insoluble portion of the cell wall, as opposed to the fraction that is released from it. We show that AmpDh3 is tetrameric both in crystals and in solution. Based on the X-ray structures of the enzyme in complex with two synthetic cell-wall-based ligands, we present for the first time a model for a multivalent anchoring of AmpDh3 onto the cell wall, which lends itself to its processive remodeling.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMPDH3	A, B	255	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: ampDh3, PA0807 EC: 3.5.1.28
UniProt
Find proteins for Q9I5D1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5D1  Go to UniProtKB:  Q9I5D1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.805	α = 90
b = 101.805	β = 90
c = 164.475	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-07-12 
• Released Date: 2013-10-09 
Deposition Author(s): Carrasco-Lopez, C., Hermoso, J.A.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Atomic model, Derived calculations, Other