4FHZ

Crystal structure of a carboxyl esterase at 2.0 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Enhanced enantioselectivity of a carboxyl esterase from Rhodobacter sphaeroides by directed evolution.

Ma, J.Wu, L.Guo, F.Gu, J.Tang, X.Jiang, L.Liu, J.Zhou, J.Yu, H.

(2013) Appl.Microbiol.Biotechnol. 97: 4897-4906

  • DOI: 10.1007/s00253-012-4396-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The present work created an esterase variant from Rhodobacter sphaeroides (RspE) with enhanced selectivity in hydrolytic kinetic resolutions by directed evolution. A "model" substrate, methyl mandelate, was introduced in the high-throughput screening ...

    The present work created an esterase variant from Rhodobacter sphaeroides (RspE) with enhanced selectivity in hydrolytic kinetic resolutions by directed evolution. A "model" substrate, methyl mandelate, was introduced in the high-throughput screening procedure. E values of a variant CH (Asn62Cys/Leu145His) for six different esters were 10-83, which were a relative improvement compared to 2-20 for the wild type. Our subsequent crystal structure interpretation and molecular dynamics simulations helped shed light on the source of enantioselectivity modified by directed evolution. Though mutations displayed no "direct" interaction with the substrate, they were hypothesized to strengthen the intramolecular interaction in the catalytic cavity of variant. Conformation analysis revealed that the enhanced enantioselectivity of variant CH for the seven substrates applied in this study was derived from the decrease in size of the substrate binding pocket.


    Organizational Affiliation

    Department of Chemical and Biological Engineering, Institute of Bioengineering, Zhejiang University, Hangzhou 310027, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase/Carboxylesterase
A
285Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)Mutation(s): 0 
Find proteins for Q3J2V1 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Go to UniProtKB:  Q3J2V1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.159 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.042α = 90.00
b = 72.042β = 90.00
c = 113.583γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
PHENIXrefinement
SHELXSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-05-29
    Type: Database references