6JD9 | pdb_00006jd9

Proteus mirabilis lipase mutant - I118V/E130G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.163 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.140 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6JD9

This is version 1.1 of the entry. See complete history

Literature

Directed evolution of a genetically encoded immobilized lipase for the efficient production of biodiesel from waste cooking oil.

Heater, B.S.Chan, W.S.Lee, M.M.Chan, M.K.

(2019) Biotechnol Biofuels 12: 165-165

  • DOI: https://doi.org/10.1186/s13068-019-1509-5
  • Primary Citation Related Structures: 
    6JD9

  • PubMed Abstract: 

    We have recently developed a one-step, genetically encoded immobilization approach based on fusion of a target enzyme to the self-crystallizing protein Cry3Aa, followed by direct production and isolation of the fusion crystals from Bacillus thuringiensis . Using this approach, Bacillus subtilis lipase A was genetically fused to Cry3Aa to produce a Cry3Aa-lipA catalyst capable of the facile conversion of coconut oil into biodiesel over 10 reaction cycles. Here, we investigate the fusion of another lipase to Cry3Aa with the goal of producing a catalyst suitable for the conversion of waste cooking oil into biodiesel. Genetic fusion of the Proteus mirabilis lipase (PML) to Cry3Aa allowed for the production of immobilized lipase crystals (Cry3Aa-PML) directly in bacterial cells. The fusion resulted in the loss of PML activity, however, and so taking advantage of its genetically encoded immobilization, directed evolution was performed on Cry3Aa-PML directly in its immobilized state in vivo. This novel strategy allowed for the selection of an immobilized PML mutant with 4.3-fold higher catalytic efficiency and improved stability. The resulting improved Cry3Aa-PML catalyst could be used to catalyze the conversion of waste cooking oil into biodiesel for at least 15 cycles with minimal loss in conversion efficiency. The genetically encoded nature of our Cry3Aa-fusion immobilization platform makes it possible to perform both directed evolution and screening of immobilized enzymes directly in vivo. This work is the first example of the use of directed evolution to optimize an enzyme in its immobilized state allowing for identification of a mutant that would unlikely have been identified from screening of its soluble form. We demonstrate that the resulting Cry3Aa-PML catalyst is suitable for the recyclable conversion of waste cooking oil into biodiesel.


  • Organizational Affiliation
    • School of Life Sciences & Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong, SAR China.

Macromolecule Content 

  • Total Structure Weight: 31.74 kDa 
  • Atom Count: 2,452 
  • Modeled Residue Count: 286 
  • Deposited Residue Count: 286 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha/beta hydrolase286Proteus mirabilisMutation(s): 2 
Gene Names: lipAM402_13560NCTC10975_00950
EC: 3.1.1.3
UniProt
Find proteins for A0A1Z1SX23 (Proteus mirabilis)
Explore A0A1Z1SX23 
Go to UniProtKB:  A0A1Z1SX23
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z1SX23
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.163 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.31α = 90
b = 65.31β = 90
c = 63.591γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hong Kong14323216

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references