6XPP | pdb_00006xpp

Crystal structure of itaconate modified Mycobaterium tuberculosis isocitrate lyase

• PDB DOI: https://doi.org/10.2210/pdb6XPP/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-08 Released: 2020-10-21 
• Deposition Author(s): Kwai, B.X.C., Bashiri, G., Leung, I.K.H.
• Funding Organization(s): Other private, Health Research Council (HRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Itaconate is a covalent inhibitor of the Mycobacterium tuberculosis isocitrate lyase.

Kwai, B.X.C., Collins, A.J., Middleditch, M.J., Sperry, J., Bashiri, G., Leung, I.K.H.

(2021) RSC Med Chem 12: 57-61

• PubMed: 34046597 
• DOI: https://doi.org/10.1039/d0md00301h
• Primary Citation Related Structures: 
  6XPP


• PubMed Abstract: 
  

  Itaconate is a mammalian antimicrobial metabolite that inhibits the isocitrate lyases (ICLs) of Mycobacterium tuberculosis . Herein, we report that ICLs form a covalent adduct with itaconate through their catalytic cysteine residue. These results reveal atomic details of itaconate inhibition and provide insights into the catalytic mechanism of ICLs.

---

Organizational Affiliation: 
• School of Chemical Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand [e-mail] [e-mail].
School of Biological Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand [e-mail].
Auckland Science Analytical Services, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand.
Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 189.25 kDa 
• Atom Count: 15,067 
• Modeled Residue Count: 1,702 
• Deposited Residue Count: 1,712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A, B, C, D	428	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: icl, Rv0467, MTV038.11 EC: 4.1.3.1
UniProt
Find proteins for P9WKK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKK7  Go to UniProtKB:  P9WKK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ITN (Subject of Investigation/LOI)	E [auth A], H [auth B], K [auth C], N [auth D]	2-methylidenebutanedioic acid C5 H6 O4 LVHBHZANLOWSRM-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.170 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.314	α = 90
b = 133.171	β = 90
c = 159.318	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Kwai, B.X.C., Bashiri, G., Leung, I.K.H.

---

Funding Organization	Location	Grant Number
Other private	New Zealand	--
Health Research Council (HRC)	New Zealand	--

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2021-06-09
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description