5XJ6

Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the glycerol 3-phosphate form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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This is version 1.1 of the entry. See complete history


Literature

Structural insights into the committed step of bacterial phospholipid biosynthesis.

Li, Z.Tang, Y.Wu, Y.Zhao, S.Bao, J.Luo, Y.Li, D.

(2017) Nat Commun 8: 1691-1691

  • DOI: https://doi.org/10.1038/s41467-017-01821-9
  • Primary Citation of Related Structures:  
    5XJ5, 5XJ6, 5XJ7, 5XJ8, 5XJ9

  • PubMed Abstract: 

    The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 Å resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of 'substrate-assisted catalysis' that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol-3-phosphate acyltransferase201Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: plsYaq_676
EC: 2.3.1
Membrane Entity: Yes 
UniProt
Find proteins for O66905 (Aquifex aeolicus (strain VF5))
Explore O66905 
Go to UniProtKB:  O66905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66905
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.148α = 90
b = 53.772β = 90
c = 87.688γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
1000 Yount Talent ProgramChina2015
National Natural Science Foundation of ChinaChina31570748
National Natural Science Foundation of ChinaChinaU1632127
Chinese Academy of Sciences Shanghai Science Research CenterChinaCAS-SSRC-YJ-2015-02
Key Program of CAS Frontier ScienceChinaQYZDB-SSW-SMC037

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references