4BXD

CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TETRASACCHARIDE PENTAPEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/ja407445x
  • Primary Citation of Related Structures:  

  • 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 do ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMPDH3
A, B
255Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: ampDh3
Find proteins for Q9I5D1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I5D1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE
C, D
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 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
MAG
Query on MAG

Download SDF File 
Download CCD File 
A, B
BETA-METHYL-N-ACETYL-D-GLUCOSAMINE
C9 H17 N O6
ZEVOCXOZYFLVKN-JGKVKWKGSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
6CL
Query on 6CL
C, D
L-PEPTIDE LINKINGC7 H15 N2 O4LYS
FGA
Query on FGA
C, D
D-gamma-peptide, C-delta linkingC5 H9 N O4

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DAL
Query on DAL
C, D
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.186α = 90.00
b = 101.186β = 90.00
c = 162.261γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PHENIXphasing
PHENIXmodel building
iMOSFLMphasing
SCALAphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Atomic model, Other