Crystal structure of wild-type SCP2 thiolase from Leishmania mexicana at 1.85 A

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Crystal Structures of Scp2-Thiolases of Trypanosomatidae, Human Pathogens Causing Widespread Tropical Diseases: The Importance for Catalysis of the Cysteine of the Unique Hdcf Loop.

Harijan, R.K.Kiema, T.-R.Karjalainen, M.P.Janardan, N.Murthy, M.R.N.Weiss, M.S.Michels, P.A.M.Wierenga, R.K.

(2013) Biochem J 455: 119

  • DOI: https://doi.org/10.1042/BJ20130669
  • Primary Citation of Related Structures:  
    3ZBG, 3ZBK, 3ZBL, 3ZBN, 4BI9, 4BIA

  • PubMed Abstract: 

    Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.

  • Organizational Affiliation

    *Department of Biochemistry, Biocenter Oulu, University of Oulu, Oulu FIN-90014, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
457Leishmania mexicanaMutation(s): 0 
Find proteins for E9AW84 (Leishmania mexicana (strain MHOM/GT/2001/U1103))
Explore E9AW84 
Go to UniProtKB:  E9AW84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9AW84
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
Q [auth B],
S [auth B]
C6 H14 O2
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
R [auth B],
T [auth B]
C2 H6 O S
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on OCS
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.249α = 90
b = 122.249β = 90
c = 133.081γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description