1VE6

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1

Bartlam, M.Wang, G.Yang, H.Gao, R.Zhao, X.Xie, G.Cao, S.Feng, Y.Rao, Z.

(2004) STRUCTURE 12: 1481-1488

  • DOI: 10.1016/j.str.2004.05.019
  • Primary Citation of Related Structures:  1VE7
  • Also Cited By: 2HU5, 2HU7, 2HU8

  • PubMed Abstract: 
  • Acylpeptide hydrolases (APH; also known as acylamino acid releasing enzyme) catalyze the removal of an N-acylated amino acid from blocked peptides. The crystal structure of an APH from the thermophilic archaeon Aeropyrum pernix K1 to 2.1 A resolution ...

    Acylpeptide hydrolases (APH; also known as acylamino acid releasing enzyme) catalyze the removal of an N-acylated amino acid from blocked peptides. The crystal structure of an APH from the thermophilic archaeon Aeropyrum pernix K1 to 2.1 A resolution confirms it to be a member of the prolyl oligopeptidase family of serine proteases. The structure of apAPH is a symmetric homodimer with each subunit comprised of two domains. The N-terminal domain is a regular seven-bladed beta-propeller, while the C-terminal domain has a canonical alpha/beta hydrolase fold and includes the active site and a conserved Ser445-Asp524-His556 catalytic triad. The complex structure of apAPH with an organophosphorus substrate, p-nitrophenyl phosphate, has also been determined. The complex structure unambiguously maps out the substrate binding pocket and provides a basis for substrate recognition by apAPH. A conserved mechanism for protein degradation from archaea to mammals is suggested by the structural features of apAPH.


    Organizational Affiliation

    Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acylamino-acid-releasing enzyme
A, B
582Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A, B
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.730α = 90.00
b = 104.739β = 90.00
c = 170.944γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance