2X3A

AsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloendopeptidase

• PDB DOI: https://doi.org/10.2210/pdb2X3A/pdb

• Classification: HYDROLASE
• Organism(s): Aeromonas salmonicida subsp. achromogenes
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-01-22 Released: 2011-02-02 
• Deposition Author(s): Bogdanovic, X., Palm, G.J., Singh, R.K., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

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

• PubMed: 27528449 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 38.02 kDa 
• Atom Count: 2,523 
• Modelled Residue Count: 293 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOXIC EXTRACELLULAR ENDOPEPTIDASE	A	343	Aeromonas salmonicida subsp. achromogenes	Mutation(s): 1  EC: 3.4.24.39
UniProt
Find proteins for Q8GMV9 (Aeromonas salmonicida subsp. achromogenes) Explore Q8GMV9  Go to UniProtKB:  Q8GMV9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.249	α = 90
b = 74.468	β = 112.35
c = 54.703	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-02 
Deposition Author(s): Bogdanovic, X., Palm, G.J., Singh, R.K., Hinrichs, W.

Revision History  

• 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
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description