2X3C

AsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloendopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Evidence of Intramolecular Propeptide Inhibition of the Aspzincin Metalloendopeptidase Asap1.

Bogdanovic, X.Palm, G.J.Schwenteit, J.Singh, R.K.Gudmundsdottir, B.K.Hinrichs, W.

(2016) FEBS Lett 590: 3280

  • DOI: 10.1002/1873-3468.12356
  • Primary Citation of Related Structures:  
    2X3A, 2X3B, 2X3C

  • PubMed Abstract: 
  • The Gram-negative bacterium Aeromonas salmonicida is a fish pathogen for various fish species worldwide. Aeromonas salmonicida subsp. achromogenes produces the extracellular, toxic zinc endopeptidase AsaP1. Crystal structure analyses at 2.0 Å resolution of two proteolytically inactive AsaP1 variants show the polypeptide folding of the protease domain and the propeptide domain ...

    The Gram-negative bacterium Aeromonas salmonicida is a fish pathogen for various fish species worldwide. Aeromonas salmonicida subsp. achromogenes produces the extracellular, toxic zinc endopeptidase AsaP1. Crystal structure analyses at 2.0 Å resolution of two proteolytically inactive AsaP1 variants show the polypeptide folding of the protease domain and the propeptide domain. These first crystal structure analyses of a precursor of a deuterolysin-like aspzincin protease provide insights into propeptide function, and specific substrate binding. A lysine side chain of the propeptide binds in the hydrophobic S1'-pocket interacting with three carboxylate side chains. An AsaP1 variant with a lysine to alanine exchange identifies the chaperone function of the propeptide.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of Asap1_E294A and Asap1_E294Q, Two Inactive Mutants of the Toxic Zinc Metallopeptidase Asap1 from Aeromonas Salmonicida Subsp. Achromogenes.
      Bogdanovic, X., Singh, R.K., Hentschke, J., Gudmundsdottir, B.K., Hinrichs, W.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 695
    • The Asap1 Peptidase of Aeromonas Salmonicida Subsp. Achromogenes is a Highly Conserved Deuterolysin Metalloprotease (Family M35) and a Major Virulence Factor.
      Arnadottir, H., Hvanndal, I., Andresdottir, V., Burr, S.E., Frey, J., Gudmundsdottir, B.K.
      (2009) J Bacteriol 191: 403
    • Isolation of a New Toxic Protease from a Strain of Aeromonas Salmonicida Subspecies Achromogenes
      Gudmundsdottir, B.K., Hastingst, S., Ellis, E.A.
      (1990) Dis Aquat Organ 9: 199

    Organizational Affiliation

    Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald, Germany. winfried.hinrichs@uni-greifswald.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TOXIC EXTRACELLULAR ENDOPEPTIDASEA343Aeromonas salmonicida subsp. achromogenesMutation(s): 1 
Gene Names: asaP1
EC: 3.4.24.39
UniProt
Find proteins for Q8GMV9 (Aeromonas salmonicida subsp. achromogenes)
Explore Q8GMV9 
Go to UniProtKB:  Q8GMV9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.958α = 90
b = 72.016β = 109.78
c = 54.996γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references, Non-polymer description, Version format compliance
  • Version 1.2: 2016-10-12
    Changes: Database references
  • Version 1.3: 2019-07-24
    Changes: Data collection