3O4H

Structure and Catalysis of Acylaminoacyl Peptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and Catalysis of Acylaminoacyl Peptidase: CLOSED AND OPEN SUBUNITS OF A DIMER OLIGOPEPTIDASE.

Harmat, V.Domokos, K.Menyhard, D.K.Pallo, A.Szeltner, Z.Szamosi, I.Beke-Somfai, T.Naray-Szabo, G.Polgar, L.

(2011) J Biol Chem 286: 1987-1998

  • DOI: 10.1074/jbc.M110.169862
  • Primary Citation of Related Structures:  
    3O4G, 3O4H, 3O4I, 3O4J

  • PubMed Abstract: 
  • Acylaminoacyl peptidase from Aeropyrum pernix is a homodimer that belongs to the prolyl oligopeptidase family. The monomer subunit is composed of one hydrolase and one propeller domain. Previous crystal structure determinations revealed that the propeller domain obstructed the access of substrate to the active site of both subunits ...

    Acylaminoacyl peptidase from Aeropyrum pernix is a homodimer that belongs to the prolyl oligopeptidase family. The monomer subunit is composed of one hydrolase and one propeller domain. Previous crystal structure determinations revealed that the propeller domain obstructed the access of substrate to the active site of both subunits. Here we investigated the structure and the kinetics of two mutant enzymes in which the aspartic acid of the catalytic triad was changed to alanine or asparagine. Using different substrates, we have determined the pH dependence of specificity rate constants, the rate-limiting step of catalysis, and the binding of substrates and inhibitors. The catalysis considerably depended both on the kind of mutation and on the nature of the substrate. The results were interpreted in terms of alterations in the position of the catalytic histidine side chain as demonstrated with crystal structure determination of the native and two mutant structures (D524N and D524A). Unexpectedly, in the homodimeric structures, only one subunit displayed the closed form of the enzyme. The other subunit exhibited an open gate to the catalytic site, thus revealing the structural basis that controls the oligopeptidase activity. The open form of the native enzyme displayed the catalytic triad in a distorted, inactive state. The mutations affected the closed, active form of the enzyme, disrupting its catalytic triad. We concluded that the two forms are at equilibrium and the substrates bind by the conformational selection mechanism.


    Organizational Affiliation

    Laboratory of Structural Chemistry and Biology and HAS-ELTE Protein Modeling Group, Institute of Chemistry, Eötvös Loránd University, Pázmány P. sétány 1/A, H-1117 Budapest, Hungary.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acylamino-acid-releasing enzymeA, B, C, D582Aeropyrum pernixMutation(s): 1 
Gene Names: APE_1547.1
EC: 3.4.19.1
UniProt
Find proteins for Q9YBQ2 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YBQ2 
Go to UniProtKB:  Q9YBQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YBQ2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.405α = 105.69
b = 97.979β = 103.52
c = 98.797γ = 100.36
Software Package:
Software NamePurpose
MAR345dtbdata 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: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-09-27
    Changes: Data collection
  • Version 1.3: 2021-10-06
    Changes: Data collection, Database references, Derived calculations