6MSO

Crystal structure of mitochondrial fumarate hydratase from Leishmania major in a complex with inhibitor thiomalate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Fumarate Hydratases from Leishmania major in a Complex with Inhibitor 2-Thiomalate.

Feliciano, P.R.Drennan, C.L.Nonato, M.C.

(2019) ACS Chem Biol 14: 266-275

  • DOI: https://doi.org/10.1021/acschembio.8b00972
  • Primary Citation of Related Structures:  
    6MSN, 6MSO

  • PubMed Abstract: 

    Leishmaniases affect the poorest people on earth and have no effective drug therapy. Here, we present the crystal structure of the mitochondrial isoform of class I fumarate hydratase (FH) from Leishmania major and compare it to the previously determined cytosolic Leishmania major isoform. We further describe the mechanism of action of the first class-specific FH inhibitor, 2-thiomalate, through X-ray crystallography and inhibition assays. Our crystal structures of both FH isoforms with inhibitor bound at 2.05 Å resolution and 1.60 Å resolution show high structural similarity. These structures further reveal that the selectivity of 2-thiomalate for class I FHs is due to direct coordination of the inhibitor to the unique Fe of the catalytic [4Fe-4S] cluster that is found in class I parasitic FHs but is absent from class II human FH. These studies provide the structural scaffold in order to exploit class I FHs as potential drug targets against leishmaniases as well as Chagas diseases, sleeping sickness, and malaria.


  • Organizational Affiliation

    Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
fumarate hydratase
A, B, C, D
585Leishmania majorMutation(s): 0 
Gene Names: LMJF_24_0320
EC: 4.2.1.2
UniProt
Find proteins for Q4QAU9 (Leishmania major)
Explore Q4QAU9 
Go to UniProtKB:  Q4QAU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QAU9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
BA [auth D],
E [auth A],
P [auth B],
V [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
AA [auth C]
DA [auth D]
K [auth A]
M [auth A]
N [auth A]
AA [auth C],
DA [auth D],
K [auth A],
M [auth A],
N [auth A],
O [auth A],
T [auth B],
U [auth B],
X [auth C],
Z [auth C]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
JYD (Subject of Investigation/LOI)
Query on JYD

Download Ideal Coordinates CCD File 
CA [auth D],
L [auth A],
S [auth B],
Y [auth C]
(2S)-2-sulfanylbutanedioic acid
C4 H6 O4 S
NJRXVEJTAYWCQJ-REOHCLBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
Q [auth B],
R [auth B],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JYD Binding MOAD:  6MSO Ki: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.741α = 90
b = 138.443β = 90
c = 138.073γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/22246-4
Sao Paulo Research Foundation (FAPESP)Brazil2013/14988-8
Sao Paulo Research Foundation (FAPESP)Brazil2008/08262-6
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM126982
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description