5XJ7

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

  • Classification: TRANSFERASE
  • Organism(s): Aquifex aeolicus (strain VF5)
  • Expression System: Escherichia coli BL21(DE3)

  • Deposited: 2017-04-30 Released: 2017-12-06 
  • Deposition Author(s): Tang, Y., Li, Z., Li, D.
  • Funding Organization(s): National Natural Science Foundation of China; Chinese Academy of Sciences (CAS)-Shanghai Science Research Center; Key Program of CAS Frontier Science; 1000 Young Talent Program; Shanghai Pujiang Talent Program 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.772 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41467-017-01821-9
  • Primary Citation of Related Structures:  

  • 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, l ...

    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

    School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China.,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.,University of Chinese Academy of Sciences, Shanghai, 201210, China.,iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China.,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. dianfan.li@sibcb.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol-3-phosphate acyltransferase
A
201Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: plsY
Find proteins for O66905 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66905
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
78M
Query on 78M

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Download CCD File 
A
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
87O
Query on 87O

Download SDF File 
Download CCD File 
A
phosphono hexadecanoate
C16 H33 O5 P
KUIJPSLAGAQZTC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.772 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.224α = 90.00
b = 65.599β = 90.00
c = 84.678γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-04-30 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Tang, Y., Li, Z., Li, D.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570748
National Natural Science Foundation of ChinaChinaU1632127
Chinese Academy of Sciences (CAS)-Shanghai Science Research CenterChinaCAS-SSRC-YJ-2015-02
Key Program of CAS Frontier ScienceChinaQYZDB-SSW-SMC037
1000 Young Talent ProgramChina2015
Shanghai Pujiang Talent ProgramChina15PJ1409400

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release