6EDW

Crystal structure of Mycobacterium tuberculosis ICL2 in the apo form

PDB DOI: https://doi.org/10.2210/pdb6EDW/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.

Macromolecule Content

Total Structure Weight: 351.09 kDa
Atom Count: 26,840
Modelled Residue Count: 2,953
Deposited Residue Count: 3,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VJU4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	E [auth A], F [auth A], J [auth C], K [auth C], N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	G [auth A] H [auth A] I [auth B] L [auth C] M [auth C] G [auth A], H [auth A], I [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]