7RB1

Isocitrate Lyase-1 from Mycobacterium tuberculosis covalently modified by 5-descarboxy-5-nitro-D-isocitric acid

Summary for 7RB1

• Entry DOI: 10.2210/pdb7rb1/pdb
• Descriptor: Isocitrate lyase, dihydroxyacetic acid, MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: tuberculosis, glyoxylate shunt, inhibitor, lyase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 4
• Total formula weight: 190231.25

Authors

Krieger, I.V.,Mellott, D.,Meek, T.,Sacchettini, J.C. (deposition date: 2021-07-05, release date: 2021-12-01, Last modification date: 2024-11-13)

Primary citation

Mellott, D.M.,Torres, D.,Krieger, I.V.,Cameron, S.A.,Moghadamchargari, Z.,Laganowsky, A.,Sacchettini, J.C.,Meek, T.D.,Harris, L.D.
Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2 R ,3 S )-2-Hydroxy-3-(nitromethyl)succinic acid.
J.Am.Chem.Soc., 143:17666-17676, 2021

PubMed Abstract: The isocitrate lyase paralogs of (ICL1 and 2) are essential for mycobacterial persistence and constitute targets for the development of antituberculosis agents. We report that (2,3)-2-hydroxy-3-(nitromethyl)succinic acid (5-NIC) undergoes apparent retro-aldol cleavage as catalyzed by ICL1 to produce glyoxylate and 3-nitropropionic acid (3-NP), the latter of which is a covalent-inactivating agent of ICL1. Kinetic analysis of this reaction identified that 5-NIC serves as a robust and efficient mechanism-based inactivator of ICL1 (/ = (1.3 ± 0.1) × 10 M s) with a partition ratio <1. Using enzyme kinetics, mass spectrometry, and X-ray crystallography, we identified that the reaction of the 5-NIC-derived 3-NP with the Cys thiolate of ICL1 results in formation of an ICL1-thiohydroxamate adduct as predicted. One aspect of the design of 5-NIC was to lower its overall charge compared to isocitrate to assist with cell permeability. Accordingly, the absence of the third carboxylate group will simplify the synthesis of pro-drug forms of 5-NIC for characterization in cell-infection models of

PubMed: 34664502
DOI: 10.1021/jacs.1c07970

Experimental method

X-RAY DIFFRACTION (1.9 Å)