4JIU

Crystal structure of the metallopeptidase zymogen of Pyrococcus abyssi abylysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M113.476580
  • Primary Citation of Related Structures:  

  • 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 o ...

    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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proabylysin
A
105Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 1 
Find proteins for Q9V1Y2 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1Y2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.620α = 90.00
b = 44.660β = 90.00
c = 72.000γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
ProDCdata collection
SCALAdata scaling
SHELXmodel building
SHELXDEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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