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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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

    Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto , Universidade de São Paulo , São Paulo 14040-903 , Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
fumarate hydrataseA, B, C, D585Leishmania majorMutation(s): 0 
Gene Names: LMJF_24_0320FH1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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-VKOJMFJBAC
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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

View Full Validation Report




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