1ZOI | pdb_00001zoi

Crystal Structure of a Stereoselective Esterase from Pseudomonas putida IFO12996


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.239 (Depositor) 
  • R-Value Work: 
    0.220 (Depositor) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZOI

This is version 1.3 of the entry. See complete history

Literature

Stereoselective esterase from Pseudomonas putida IFO12996 reveals alpha/beta hydrolase folds for D-beta-acetylthioisobutyric acid synthesis

Elmi, F.Lee, H.T.Huang, J.Y.Hsieh, Y.C.Wang, Y.L.Chen, Y.J.Shaw, S.Y.Chen, C.J.

(2005) J Bacteriol 187: 8470-8476

  • DOI: https://doi.org/10.1128/JB.187.24.8470-8476.2005
  • Primary Citation Related Structures: 
    1ZOI

  • PubMed Abstract: 

    Esterase (EST) from Pseudomonas putida IFO12996 catalyzes the stereoselective hydrolysis of methyl dl-beta-acetylthioisobutyrate (dl-MATI) to produce d-beta-acetylthioisobutyric acid (DAT), serving as a key intermediate for the synthesis of angiotensin-converting enzyme inhibitors. The EST gene was cloned and expressed in Escherichia coli; the recombinant protein is a non-disulfide-linked homotrimer with a monomer molecular weight of 33,000 in both solution and crystalline states, indicating that these ESTs function as trimers. EST hydrolyzed dl-MATI to produce DAT with a degree of conversion of 49.5% and an enantiomeric excess value of 97.2% at an optimum pH of about 8 to 10 and an optimum temperature of about 57 to 67 degrees C. The crystal structure of EST has been determined by X-ray diffraction to a resolution of 1.6 A, confirming that EST is a member of the alpha/beta hydrolase fold superfamily of enzymes and includes a catalytic triad of Ser97, Asp227, and His256. The active site is located approximately in the middle of the molecule at the end of a pocket approximately 12 A deep. EST can hydrolyze the methyl ester group without affecting the acetylthiol ester moiety in dl-MATI. The examination of substrate specificity of EST toward other linear esters revealed that the enzyme showed specific activity toward methyl esters and that it recognized the configuration at C-2.


  • Organizational Affiliation
    • Life Science Group, National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 90.61 kDa 
  • Atom Count: 6,694 
  • Modeled Residue Count: 824 
  • Deposited Residue Count: 828 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
esterase
A, B, C
276Pseudomonas putidaMutation(s): 0 
EC: 3.1
UniProt
Find proteins for Q3HWU8 (Pseudomonas putida)
Explore Q3HWU8 
Go to UniProtKB:  Q3HWU8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3HWU8
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.239 (Depositor) 
  • R-Value Work:  0.220 (Depositor) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.556α = 90
b = 98.108β = 90
c = 153.63γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALAdata scaling
CNSrefinement
HKL-2000data reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references