Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 252764.63 
• Atom Count: 17239 
• Residue Count: 2328 
• Unique protein chains: 1

3O4H

Structure and Catalysis of Acylaminoacyl Peptidase

• DOI: 10.2210/pdb3O4H/pdb

• Classification: HYDROLASE
• Organism(s): Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2010-07-27 Released: 2010-11-17 
• Deposition Author(s): Harmat, V., Domokos, K., Menyhard, D.K., Pallo, A., Szeltner, Z., Szamosi, I., Beke-Somfai, T., Naray-Szabo, G., Polgar, L.

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Experimental Data Snapshot

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

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

• PubMed: 21084296 
• DOI: 10.1074/jbc.M110.169862
• Primary Citation of Related Structures:  
  3O4J, 3O4I, 3O4G


• 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. 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.

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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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Acylamino-acid-releasing enzyme	A, B, C, D	582	Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)	Mutations: A524D EC: 3.4.19.1
Find proteins for Q9YBQ2 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Go to UniProtKB:  Q9YBQ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	B, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
GOL	A, B, D	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.234 
• R-Value Work: 0.203 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 71.405	α = 105.69
b = 97.979	β = 103.52
c = 98.797	γ = 100.36

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
XDS	data reduction
XSCALE	data scaling
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-27 
• Released Date: 2010-11-17 
• Deposition Author(s): Harmat, V., Domokos, K., Menyhard, D.K., Pallo, A., Szeltner, Z., Szamosi, I., Beke-Somfai, T., Naray-Szabo, G., Polgar, L.

Revision History 

• Version 1.0: 2010-11-17
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-09-27
  Type: Data collection