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 

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This is version 1.6 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: 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.


Macromolecules
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
EC: 3.4.19.1
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y3A
Query on Y3A
Download Ideal Coordinates CCD File 
B
N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide
C22 H26 Cl N3 O5
WLEADEPGUSFGIL-OALUTQOASA-N
HEZ
Query on HEZ
Download Ideal Coordinates CCD File 
H [auth B]
I [auth B]
J [auth B]
K [auth B]
L [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
CL
Query on CL
Download Ideal Coordinates CCD File 
R [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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
Biologically Interesting Molecules (External Reference) 1 Unique
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

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Ligand Structure Quality Assessment 


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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
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2023-10-18
    Changes: Structure summary
  • Version 1.6: 2024-03-13
    Changes: Source and taxonomy