Pyrococcus horikoshii acylaminoacyl peptidase (uncomplexed)

Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION.

Menyhard, D.K.Kiss-Szeman, A.Tichy-Racs, E.Hornung, B.Radi, K.Szeltner, Z.Domokos, K.Szamosi, I.Naray-Szabo, G.Polgar, L.Harmat, V.

(2013) J Biol Chem 288: 17884-17894

  • DOI: https://doi.org/10.1074/jbc.M113.451534
  • Primary Citation of Related Structures:  
    4HXE, 4HXF, 4HXG

  • PubMed Abstract: 

    Oligopeptidases impose a size limitation on their substrates, the mechanism of which has long been under debate. Here we present the structure of a hexameric serine protease, an oligopeptidase from Pyrococcus horikoshii (PhAAP), revealing a complex, self-compartmentalized inner space, where substrates may access the monomer active sites passing through a double-gated "check-in" system, first passing through a pore on the hexamer surface and then turning to enter through an even smaller opening at the monomers' domain interface. This substrate screening strategy is unique within the family. We found that among oligopeptidases, a residue of the catalytic apparatus is positioned near an amylogenic β-edge, which needs to be protected to prevent aggregation, and we found that different oligopeptidases use different strategies to achieve such an end. We propose that self-assembly within the family results in characteristically different substrate selection mechanisms coupled to different multimerization states.

  • Organizational Affiliation

    Protein Modeling Research Group, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein PH0594A [auth B]622Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH0594
Find proteins for O58323 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58323 
Go to UniProtKB:  O58323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58323
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183α = 90
b = 183β = 90
c = 144.63γ = 120
Software Package:
Software NamePurpose
bioteXdata collection
SHELXmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2013-07-03
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations