5L2R

Crystal structure of fumarate hydratase from Leishmania major

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold.

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

(2016) Proc Natl Acad Sci U S A 113: 9804-9809

  • DOI: 10.1073/pnas.1605031113
  • Primary Citation of Related Structures:  
    5L2R

  • PubMed Abstract: 

    • Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster ...

    Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster. Our 2.05 Å resolution data further reveal a dimeric architecture for this FH that resembles a heart, with each lobe comprised of two domains that are arranged around the active site. Besides the active site, where the substrate S-malate is bound bidentate to the unique iron of the [4Fe-4S] cluster, other binding pockets are found near the dimeric enzyme interface, some of which are occupied by malonate, shown here to be a weak inhibitor of this enzyme. Taken together, these data provide a framework both for investigations of the class I FH catalytic mechanism and for drug design aimed at fighting neglected tropical diseases.

    Organizational Affiliation: 

    Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo 14040-903, Brazil; cdrennan@mit.edu cristy@fcfrp.usp.br.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate hydrataseA, B604Leishmania majorMutation(s): 0 
Gene Names: LMJF_29_1960, FH2
EC: 4.2.1.2
UniProt
Find proteins for E9AE57 (Leishmania major)
Explore E9AE57 
Go to UniProtKB:  E9AE57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9AE57
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
J [auth A],
U [auth B]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
LMR
Query on LMR
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B]		(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
T [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
MLA
Query on MLA
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
M [auth B],
N [auth B]		MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
O [auth B],
P [auth B],
G [auth A],
H [auth A],
I [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LMR Binding MOAD:  5L2R IC50: 9.80e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.675α = 90
b = 85.128β = 90
c = 241.476γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2009/10454-3
Sao Paulo Research Foundation (FAPESP)Brazil2011/19674-6
Sao Paulo Research Foundation (FAPESP)Brazil2008/08262-6
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2016-09-07
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2019-11-20
    Changes: Author supporting evidence