The crystal structure of Cyclopropane-fatty-acyl-phospholipid synthase from Lactobacillus acidophilus

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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Crystal structure of bacterial cyclopropane-fatty-acyl-phospholipid synthase with phospholipid.

Ma, Y.Pan, C.Wang, Q.

(2019) J Biochem 166: 139-147

  • DOI: https://doi.org/10.1093/jb/mvz018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The lipids containing cyclopropane-fatty-acid (CFA) protect bacteria from adverse conditions such as acidity, freeze-drying desiccation and exposure to pollutants. CFA is synthesized when cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase, CFAS) transfers a methylene group from S-adenosylmethionine (SAM) across the cis double bonds of unsaturated fatty acyl chains. Here, we reported a 2.7-Å crystal structure of CFAS from Lactobacillus acidophilus. The enzyme is composed of N- and C-terminal domain, which belong to the sterol carrier protein and methyltransferase superfamily, respectively. A phospholipid in the substrate binding site and a bicarbonate ion (BCI) acting as a general base in the active site were discovered. To elucidate the mechanism, a docking experiment using CFAS from L. acidophilus and SAM was carried out. The analysis of this structure demonstrated that three groups, the carbons from the substrate, the BCI and the methyl of S(CHn)3 group, were close enough to form a cyclopropane ring with the help of amino acids in the active site. Therefore, the structure supports the hypothesis that CFAS from L. acidophilus catalyzes methyl transfer via a carbocation mechanism. These findings provide a structural basis to more deeply understand enzymatic cyclopropanation.

  • Organizational Affiliation

    School of Bioengineering, Jingchu University of Technology, Jingmen, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclopropane-fatty-acyl-phospholipid synthase
A, B
399Lactobacillus acidophilus NCFMMutation(s): 0 
Gene Names: LBA1274
Find proteins for Q5FJM0 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM))
Explore Q5FJM0 
Go to UniProtKB:  Q5FJM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FJM0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.982α = 90
b = 120.982β = 90
c = 163.487γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PDBSETdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Hubei Natural Science Foundation of ChinaChina2015ZFB763
the research fund from JCUTChinaZR201410

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description