1M7J

Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of D-Aminoacylase from Alcaligenes faecalis DA1. A NOVEL SUBSET OF AMIDOHYDROLASES AND INSIGHTS INTO THE ENZYME MECHANISM.

Liaw, S.-H.Chen, S.-J.Ko, T.-P.Hsu, C.-S.Chen, C.J.Wang, A.H.Tsai, Y.-C.

(2003) J.Biol.Chem. 278: 4957-4962

  • DOI: 10.1074/jbc.M210795200
  • Also Cited By: 1RJP, 1RJQ, 1RJR, 1RK5, 1RK6, 1V4Y, 1V51

  • PubMed Abstract: 
  • D-Aminoacylase is an attractive candidate for commercial production of D-amino acids through its catalysis in the hydrolysis of N-acyl-D-amino acids. We report here the first D-aminoacylase crystal structure from A. faecalis at 1.5-A resolution. The ...

    D-Aminoacylase is an attractive candidate for commercial production of D-amino acids through its catalysis in the hydrolysis of N-acyl-D-amino acids. We report here the first D-aminoacylase crystal structure from A. faecalis at 1.5-A resolution. The protein comprises a small beta-barrel, and a catalytic (betaalpha)(8)-barrel with a 63-residue insertion. The enzyme structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrels superimpose well. Unexpectedly, the enzyme binds two zinc ions with widely different affinities, although only the tightly bound zinc ion is required for activity. One zinc ion is coordinated by Cys(96), His(220), and His(250), while the other is loosely chelated by His(67), His(69), and Cys(96). This is the first example of the metal ion coordination by a cysteine residue in the superfamily. Therefore, D-aminoacylase defines a novel subset and is a mononuclear zinc metalloenzyme but containing a binuclear active site. The preferred substrate was modeled into a hydrophobic pocket, revealing the substrate specificity and enzyme catalysis. The 63-residue insertion containing substrate-interacting residues may act as a gate controlling access to the active site, revealing that the substrate binding would induce a closed conformation to sequester the catalysis from solvent.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of a D-aminoacylase from Alcaligenes faecalis DA1
      Hsu, C.-S.,Chen, S.-J.,Tsai, Y.-C.,Lin, T.-W.,Liaw, S.-H.,Wang, A.H.
      (2002) Acta Crystallogr.,Sect.D 58: 1482
    • Structural-based mutational analysis of D-aminoacylase from Alcaligenes faecalis DA1.
      Hsu, C.-S.,Lai, W.-L.,Chang, W.-W.,Liaw, S.-H.,Tsai, Y.-C.
      (2002) Protein Sci. 11: 2545


    Organizational Affiliation

    Department of Life Science, Institute of Biochemistry, National Yang-Ming University, Taipei 11221, Taiwan. shliaw@ym.edu.tw




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-aminoacylase
A
484Alcaligenes faecalisEC: 3.5.1.81
Find proteins for Q9AGH8 (Alcaligenes faecalis)
Go to UniProtKB:  Q9AGH8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.102α = 90.00
b = 77.167β = 90.00
c = 135.744γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
CNSphasing
WARPmodel building
ARP/wARPmodel building
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description