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), 0.190 (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 of 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].

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 
• Modelled 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), 0.190 (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