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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fumarate hydrataseA, B604Leishmania majorMutation(s): 0 
Gene Names: LMJF_29_1960FH2
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

View Full Validation Report




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