4FTW

Crystal structure of a carboxyl esterase N110C/L145H at 2.3 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

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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:  
    4FHZ, 4FTW

  • 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 procedure ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase/CarboxylesteraseA285Cereibacter sphaeroides 2.4.1Mutation(s): 2 
Gene Names: CGMCC1.1737RHOS4_13150RSP_2728
EC: 3.1.1.1
UniProt
Find proteins for Q3J2V1 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J2V1 
Go to UniProtKB:  Q3J2V1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3J2V1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3CM
Query on 3CM

Download Ideal Coordinates CCD File 
C [auth A]3-CYCLOHEXYLPROPYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE
C21 H38 O11
FDBLAHXBTQUZSM-ZESVGKPKSA-N
 Ligand Interaction
PIN
Query on PIN

Download Ideal Coordinates CCD File 
B [auth A]PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
C8 H18 N2 O6 S2
IHPYMWDTONKSCO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.382α = 90
b = 112.382β = 90
c = 47.569γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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