7RB1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2 R ,3 S )-2-Hydroxy-3-(nitromethyl)succinic acid.

Mellott, D.M.Torres, D.Krieger, I.V.Cameron, S.A.Moghadamchargari, Z.Laganowsky, A.Sacchettini, J.C.Meek, T.D.Harris, L.D.

(2021) J Am Chem Soc 143: 17666-17676

  • DOI: 10.1021/jacs.1c07970
  • Primary Citation of Related Structures:  
    7RB1

  • PubMed Abstract: 
  • The isocitrate lyase paralogs of Mycobacterium tuberculosis (ICL1 and 2) are essential for mycobacterial persistence and constitute targets for the development of antituberculosis agents. We report that (2 R ,3 S )-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 ...

    The isocitrate lyase paralogs of Mycobacterium tuberculosis (ICL1 and 2) are essential for mycobacterial persistence and constitute targets for the development of antituberculosis agents. We report that (2 R ,3 S )-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 ( k inact / K I = (1.3 ± 0.1) × 10 3 M -1 s -1 ) 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 191 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 M. tuberculosis.


    Organizational Affiliation

    The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate lyaseA, B, C, D428Mycobacterium tuberculosisMutation(s): 0 
Gene Names: iclRv0467MTV038.11
EC: 4.1.3.1
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
54I (Subject of Investigation/LOI)
Query on 54I

Download Ideal Coordinates CCD File 
AA [auth D],
H [auth A],
O [auth B],
U [auth C]
(3E)-3-(hydroxyimino)propanoic acid
C3 H5 N O3
XTKKYEXSKPSWOJ-DUXPYHPUSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
BA [auth D],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
V [auth C],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
48J
Query on 48J

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
R [auth C]
dihydroxyacetic acid
C2 H4 O4
GOCCREQJUBABAL-UHFFFAOYSA-N
 Ligand Interaction
GLV
Query on GLV

Download Ideal Coordinates CCD File 
X [auth D]GLYOXYLIC ACID
C2 H2 O3
HHLFWLYXYJOTON-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth B],
N [auth B],
S [auth C],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.068α = 90
b = 140.301β = 90
c = 160.693γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release