7RBX

Crystal structure of isocitrate lyase and phosphorylmutase:isocitrate lyase from Brucella melitensis biovar Abortus 2308 bound to itaconic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Aconitate decarboxylase 1 participates in the control of pulmonary Brucella infection in mice.

Demars, A.Vitali, A.Comein, A.Carlier, E.Azouz, A.Goriely, S.Smout, J.Flamand, V.Van Gysel, M.Wouters, J.Abendroth, J.Edwards, T.E.Machelart, A.Hoffmann, E.Brodin, P.De Bolle, X.Muraille, E.

(2021) PLoS Pathog 17: e1009887-e1009887

  • DOI: https://doi.org/10.1371/journal.ppat.1009887
  • Primary Citation of Related Structures:  
    7RBX

  • PubMed Abstract: 

    Brucellosis is one of the most widespread bacterial zoonoses worldwide. Here, our aim was to identify the effector mechanisms controlling the early stages of intranasal infection with Brucella in C57BL/6 mice. During the first 48 hours of infection, alveolar macrophages (AMs) are the main cells infected in the lungs. Using RNA sequencing, we identified the aconitate decarboxylase 1 gene (Acod1; also known as Immune responsive gene 1), as one of the genes most upregulated in murine AMs in response to B. melitensis infection at 24 hours post-infection. Upregulation of Acod1 was confirmed by RT-qPCR in lungs infected with B. melitensis and B. abortus. We observed that Acod1-/- C57BL/6 mice display a higher bacterial load in their lungs than wild-type (wt) mice following B. melitensis or B. abortus infection, demonstrating that Acod1 participates in the control of pulmonary Brucella infection. The ACOD1 enzyme is mostly produced in mitochondria of macrophages, and converts cis-aconitate, a metabolite in the Krebs cycle, into itaconate. Dimethyl itaconate (DMI), a chemically-modified membrane permeable form of itaconate, has a dose-dependent inhibitory effect on Brucella growth in vitro. Interestingly, structural analysis suggests the binding of itaconate into the binding site of B. abortus isocitrate lyase. DMI does not inhibit multiplication of the isocitrate lyase deletion mutant ΔaceA B. abortus in vitro. Finally, we observed that, unlike the wt strain, the ΔaceA B. abortus strain multiplies similarly in wt and Acod1-/- C57BL/6 mice. These data suggest that bacterial isocitrate lyase might be a target of itaconate in AMs.


  • Organizational Affiliation

    Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur, Namur, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrase
A, B, C, D
450Brucella abortus 2308Mutation(s): 0 
Gene Names: BAB1_1631
EC: 4.1.3.1
UniProt
Find proteins for Q2YQA0 (Brucella abortus (strain 2308))
Explore Q2YQA0 
Go to UniProtKB:  Q2YQA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YQA0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ITN (Subject of Investigation/LOI)
Query on ITN

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
O [auth C],
R [auth D]
2-methylidenebutanedioic acid
C5 H6 O4
LVHBHZANLOWSRM-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
S [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
I [auth A]
J [auth A]
K [auth A]
N [auth C]
E [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth C],
T [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
P [auth C],
Q [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.75α = 90
b = 136.27β = 90
c = 181.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description