5AZB

Crystal structure of Escherichia coli Lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of E. coli lipoprotein diacylglyceryl transferase

Mao, G.Zhao, Y.Kang, X.Li, Z.Zhang, Y.Wang, X.Sun, F.Sankaran, K.Zhang, X.C.

(2016) Nat Commun 7: 10198-10198

  • DOI: https://doi.org/10.1038/ncomms10198
  • Primary Citation of Related Structures:  
    5AZB, 5AZC

  • PubMed Abstract: 

    Lipoprotein biogenesis is essential for bacterial survival. Phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (Lgt) is an integral membrane enzyme that catalyses the first reaction of the three-step post-translational lipid modification. Deletion of the lgt gene is lethal to most Gram-negative bacteria. Here we present the crystal structures of Escherichia coli Lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid at 1.9 and 1.6 Å resolution, respectively. The structures reveal the presence of two binding sites and support the previously reported structure-function relationships of Lgt. Complementation results of lgt-knockout cells with different mutant Lgt variants revealed critical residues, including Arg143 and Arg239, that are essential for diacylglyceryl transfer. Using a GFP-based in vitro assay, we correlated the activities of Lgt with structural observations. Together, the structural and biochemical data support a mechanism whereby substrate and product, lipid-modified lipobox-containing peptide, enter and leave the enzyme laterally relative to the lipid bilayer.


  • Organizational Affiliation

    National Laboratory of Macromolecules, National Center of Protein Science - Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prolipoprotein diacylglyceryl transferase300Escherichia coli K-12Mutation(s): 0 
Gene Names: lgtumpAb2828JW2796
EC: 2.4.99 (PDB Primary Data), 2.5.1.145 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P60955 (Escherichia coli (strain K12))
Explore P60955 
Go to UniProtKB:  P60955
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60955
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGT
Query on PGT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
D [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.413α = 90
b = 60.973β = 90
c = 117.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Data collection
  • Version 1.2: 2020-02-26
    Changes: Data collection, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references, Structure summary