4HXF

Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 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 ...

    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.


    Related Citations: 
    • Characterization of a novel acylaminoacyl peptidase with hexameric structure and endopeptidase activity.
      Szeltner, Z., Kiss, A.L., Domokos, K., Harmat, V., Naray-Szabo, G., Polgar, L.
      (2009) Biochim Biophys Acta 1794: 1204

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized protein PH0594A [auth B]622Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH0594
EC: 3.4.19.1
Find proteins for O58323 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58323 
Go to UniProtKB:  O58323
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y3A
Query on Y3A

Download Ideal Coordinates CCD File 
BN-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide
C22 H26 Cl N3 O5
WLEADEPGUSFGIL-OALUTQOASA-N
 Ligand Interaction
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
H [auth B] , I [auth B] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , O [auth B] , 
H [auth B],  I [auth B],  J [auth B],  K [auth B],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
R [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth B], D [auth B], E [auth B], F [auth B], G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001053 (Y3A)
Query on PRD_001053
BZ-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM)Peptide-like /  Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.057α = 90
b = 184.057β = 90
c = 145.529γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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: 2014-10-08
    Changes: Non-polymer description