Crystal structure of the metallopeptidase zymogen of Pyrococcus abyssi abylysin

Experimental Data Snapshot

  • Resolution: 1.15 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 

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A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases

Lopez-Pelegrin, M.Cerda-Costa, N.Martinez-Jimenez, F.Cintas-Pedrola, A.Canals, A.Peinado, J.R.Marti-Renom, M.A.Lopez-Otin, C.Arolas, J.L.Gomis-Ruth, F.X.

(2013) J Biol Chem 288: 21279-21294

  • DOI: https://doi.org/10.1074/jbc.M113.476580
  • Primary Citation of Related Structures:  
    4JIU, 4JIX

  • PubMed Abstract: 

    In the search for structural models of integral-membrane metallopeptidases (MPs), we discovered three related proteins from thermophilic prokaryotes, which we grouped into a novel family called "minigluzincins." We determined the crystal structures of the zymogens of two of these (Pyrococcus abyssi proabylysin and Methanocaldococcus jannaschii projannalysin), which are soluble and, with ∼100 residues, constitute the shortest structurally characterized MPs to date. Despite relevant sequence and structural similarity, the structures revealed two unique mechanisms of latency maintenance through the C-terminal segments previously unseen in MPs as follows: intramolecular, through an extended tail, in proabylysin, and crosswise intermolecular, through a helix swap, in projannalysin. In addition, structural and sequence comparisons revealed large similarity with MPs of the gluzincin tribe such as thermolysin, leukotriene A4 hydrolase relatives, and cowrins. Noteworthy, gluzincins mostly contain a glutamate as third characteristic zinc ligand, whereas minigluzincins have a histidine. Sequence and structural similarity further allowed us to ascertain that minigluzincins are very similar to the catalytic domains of integral membrane MPs of the MEROPS database families M48 and M56, such as FACE1, HtpX, Oma1, and BlaR1/MecR1, which are provided with trans-membrane helices flanking or inserted into a minigluzincin-like catalytic domain. In a time where structural biochemistry of integral-membrane proteins in general still faces formidable challenges, the minigluzincin soluble minimal scaffold may contribute to our understanding of the working mechanisms of these membrane MPs and to the design of novel inhibitors through structure-aided rational drug design approaches.

  • Organizational Affiliation

    the Genome Biology Group, Centre Nacional d'Anàlisi Genòmic, c/Baldiri Reixac, 4, 08028 Barcelona,; the Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation, c/Dr. Aiguader, 88, 08003 Barcelona.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proabylysin105Pyrococcus abyssi GE5Mutation(s): 1 
Gene Names: PAB3079PYRAB02920
Find proteins for Q9V1Y2 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V1Y2 
Go to UniProtKB:  Q9V1Y2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V1Y2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.15 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.62α = 90
b = 44.66β = 90
c = 72γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
SHELXmodel building
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description, Structure summary