6EE1

Crystal structure of Mycobacterium tuberculosis ICL2 in complex with acetyl-CoA

• PDB DOI:  https://doi.org/10.2210/pdb6EE1/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis CDC1551
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-12 Released: 2019-08-14 
• Deposition Author(s): Bashiri, G., Bhusal, R., Leung, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.232 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2.

Bhusal, R.P., Jiao, W., Kwai, B.X.C., Reynisson, J., Collins, A.J., Sperry, J., Bashiri, G., Leung, I.K.H.

(2019) Nat Commun 10: 4639-4639

• PubMed: 31604954 
• DOI: https://doi.org/10.1038/s41467-019-12614-7
• Primary Citation of Related Structures:  
  6EDW, 6EDZ, 6EE1


• PubMed Abstract: 
  

Isocitrate lyase is important for lipid utilisation by Mycobacterium tuberculosis but its ICL2 isoform is poorly understood. Here we report that binding of the lipid metabolites acetyl-CoA or propionyl-CoA to ICL2 induces a striking structural rearrangement, substantially increasing isocitrate lyase and methylisocitrate lyase activities. Thus, ICL2 plays a pivotal role regulating carbon flux between the tricarboxylic acid (TCA) cycle, glyoxylate shunt and methylcitrate cycle at high lipid concentrations, a mechanism essential for bacterial growth and virulence.

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Organizational Affiliation: 

Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 353.74 kDa 
• Atom Count: 23,629 
• Modelled Residue Count: 2,900 
• Deposited Residue Count: 3,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase 2	A, B, C, D	786	Mycobacterium tuberculosis CDC1551	Mutation(s): 0  Gene Names: icl2, aceA-2, MT1966 EC: 4.1.3.1
UniProt
Find proteins for Q8VJU4 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Explore Q8VJU4  Go to UniProtKB:  Q8VJU4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	E [auth A], G [auth B], I [auth C], K [auth D]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.232 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.475	α = 90
b = 169.972	β = 95.26
c = 106.425	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Bashiri, G., Bhusal, R., Leung, I.

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-10-23
  Changes: Data collection, Database references