Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

Starting Model: experimental
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Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis.

Pham, T.V.Murkin, A.S.Moynihan, M.M.Harris, L.Tyler, P.C.Shetty, N.Sacchettini, J.C.Huang, H.L.Meek, T.D.

(2017) Proc Natl Acad Sci U S A 114: 7617-7622

  • DOI: https://doi.org/10.1073/pnas.1706134114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Isocitrate lyase (ICL, types 1 and 2) is the first enzyme of the glyoxylate shunt, an essential pathway for Mycobacterium tuberculosis ( Mtb ) during the persistent phase of human TB infection. Here, we report 2-vinyl-d-isocitrate (2-VIC) as a mechanism-based inactivator of Mtb ICL1 and ICL2. The enzyme-catalyzed retro-aldol cleavage of 2-VIC unmasks a Michael substrate, 2-vinylglyoxylate, which then forms a slowly reversible, covalent adduct with the thiolate form of active-site Cys 191 2-VIC displayed kinetic properties consistent with covalent, mechanism-based inactivation of ICL1 and ICL2 with high efficiency (partition ratio, <1). Analysis of a complex of ICL1:2-VIC by electrospray ionization mass spectrometry and X-ray crystallography confirmed the formation of the predicted covalent S -homopyruvoyl adduct of the active-site Cys 191 .

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate lyase 1
A, B, C, D
428Mycobacterium tuberculosis str. Erdman = ATCC 35801Mutation(s): 0 
Gene Names: icl1ERDMAN_0512Q643_00485
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P9WKK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKK7 
Go to UniProtKB:  P9WKK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKK7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.78 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.086α = 90
b = 129.236β = 90
c = 167.952γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
SCALEPACKdata scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Advisory, Database references, Derived calculations
  • Version 1.2: 2017-07-26
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description