3LQ0

Zymogen structure of crayfish astacin metallopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Proenzyme structure and activation of astacin metallopeptidase

Guevara, T.Yiallouros, I.Kappelhoff, R.Bissdorf, S.Stocker, W.Gomis-Ruth, F.X.

(2010) J Biol Chem 285: 13958-13965

  • DOI: https://doi.org/10.1074/jbc.M109.097436
  • Primary Citation of Related Structures:  
    3LQ0

  • PubMed Abstract: 

    Proteolysis is regulated by inactive (latent) zymogens, with a prosegment preventing access of substrates to the active-site cleft of the enzyme. How latency is maintained often depends on the catalytic mechanism of the protease. For example, in several families of the metzincin metallopeptidases, a "cysteine switch" mechanism involves a conserved prosegment motif with a cysteine residue that coordinates the catalytic zinc ion. Another family of metzincins, the astacins, do not possess a cysteine switch, so latency is maintained by other means. We have solved the high resolution crystal structure of proastacin from the European crayfish, Astacus astacus. Its prosegment is the shortest structurally reported for a metallopeptidase, and it has a unique structure. It runs through the active-site cleft in reverse orientation to a genuine substrate. Moreover, a conserved aspartate, projected by a wide loop of the prosegment, coordinates the zinc ion instead of the catalytic solvent molecule found in the mature enzyme. Activation occurs through two-step limited proteolysis and entails major rearrangement of a flexible activation domain, which becomes rigid and creates the base of the substrate-binding cleft. Maturation also requires the newly formed N terminus to be precisely trimmed so that it can participate in a buried solvent-mediated hydrogen-bonding network, which includes an invariant active-site residue. We describe a novel mechanism for latency and activation, which shares some common features both with other metallopeptidases and with serine peptidases.


  • Organizational Affiliation

    Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona Science Park, Helix Building, c/Baldiri Reixac 15-21, E-08028, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ProAstacin235Astacus astacusMutation(s): 2 
EC: 3.4.24.21
UniProt
Find proteins for P07584 (Astacus astacus)
Explore P07584 
Go to UniProtKB:  P07584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07584
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.91α = 90
b = 63.37β = 90
c = 69.19γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-19
    Changes: Refinement description
  • Version 1.3: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.4: 2021-11-10
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2023-11-01
    Changes: Data collection, Refinement description