Crystal structure of cytosolic fumarate hydratase from Leishmania major in a complex with malonate

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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Structural and Biochemical Investigations of the [4Fe-4S] Cluster-Containing Fumarate Hydratase fromLeishmania major.

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

(2019) Biochemistry 58: 5011-5021

  • DOI: https://doi.org/10.1021/acs.biochem.9b00923
  • Primary Citation of Related Structures:  
    6UNZ, 6UO0, 6UOI, 6UOJ, 6UP9, 6UPM, 6UPO, 6UQ8, 6UQ9, 6UQB, 6UQL, 6UQM, 6UQN

  • PubMed Abstract: 

    Class I fumarate hydratases (FHs) are central metabolic enzymes that use a [4Fe-4S] cluster to catalyze the reversible conversion of fumarate to S -malate. The parasite Leishmania major , which is responsible for leishmaniasis, expresses two class I FH isoforms: mitochondrial LmFH-1 and cytosolic LmFH-2. In this study, we present kinetic characterizations of both LmFH isoforms, present 13 crystal structures of LmFH-2 variants, and employ site-directed mutagenesis to investigate the enzyme's mechanism. Our kinetic data confirm that both LmFH-1 and LmFH-2 are susceptible to oxygen-dependent inhibition, with data from crystallography and electron paramagnetic resonance spectroscopy showing that oxygen exposure converts an active [4Fe-4S] cluster to an inactive [3Fe-4S] cluster. Our anaerobically conducted kinetic studies reveal a preference for fumarate over S -malate. Our data further reveal that single alanine substitutions of T467, R421, R471, D135, and H334 decrease k cat values 9-16000-fold without substantially affecting K m values, suggesting that these residues function in catalytic roles. Crystal structures of LmFH-2 variants are consistent with this idea, showing similar bidentate binding to the unique iron of the [4Fe-4S] cluster for substrate S -malate as observed in wild type FH. We further present LmFH-2 structures with substrate fumarate and weak inhibitors succinate and malonate bound in the active site and the first structure of an LmFH that is substrate-free and inhibitor-free, the latter showing increased mobility in the C-terminal domain. Collectively, these data provide insight into the molecular basis for the reaction catalyzed by LmFHs, enzymes that are potential drug targets against leishmaniasis.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fumarate hydratase 2
A, B
604Leishmania major strain FriedlinMutation(s): 0 
Gene Names: FH2LMJF_29_1960
Find proteins for E9AE57 (Leishmania major)
Explore E9AE57 
Go to UniProtKB:  E9AE57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9AE57
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F3S (Subject of Investigation/LOI)
Query on F3S

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
Fe3 S4
MLA (Subject of Investigation/LOI)
Query on MLA

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C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B]
C3 H4 O4
Query on GOL

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C3 H8 O3
FE (Subject of Investigation/LOI)
Query on FE

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H [auth A],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.578α = 90
b = 85.102β = 90
c = 240.231γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description