1M7J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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
  • Primary Citation of Related Structures:  
    1M7J

  • 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 protein comprises a small beta-barrel, and a catalytic (betaalpha)(8)-barrel with a 63-residue insertion ...

    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: 
    • 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
    • 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 D Biol Crystallogr 58: 1482

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-aminoacylaseA484Alcaligenes faecalisMutation(s): 0 
EC: 3.5.1.81
UniProt
Find proteins for Q9AGH8 (Alcaligenes faecalis)
Explore Q9AGH8 
Go to UniProtKB:  Q9AGH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AGH8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.102α = 90
b = 77.167β = 90
c = 135.744γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
WARPmodel building
HKL-2000data reduction
CNSphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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