Crystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant with acetyl-CoA.

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Crystallographic substrate binding studies of Leishmania mexicana SCP2-thiolase (type-2): unique features of oxyanion hole-1.

Harijan, R.K.Kiema, T.R.Syed, S.M.Qadir, I.Mazet, M.Bringaud, F.Michels, P.A.M.Wierenga, R.K.

(2017) Protein Eng Des Sel 30: 225-233

  • DOI: https://doi.org/10.1093/protein/gzw080
  • Primary Citation of Related Structures:  
    5LNQ, 5LOT

  • PubMed Abstract: 

    Structures of the C123A variant of the dimeric Leishmania mexicana SCP2-thiolase (type-2) (Lm-thiolase), complexed with acetyl-CoA and acetoacetyl-CoA, respectively, are reported. The catalytic site of thiolase contains two oxyanion holes, OAH1 and OAH2, which are important for catalysis. The two structures reveal for the first time the hydrogen bond interactions of the CoA-thioester oxygen atom of the substrate with the hydrogen bond donors of OAH1 of a CHH-thiolase. The amino acid sequence fingerprints ( xS, EAF, G P) of three catalytic loops identify the active site geometry of the well-studied CNH-thiolases, whereas SCP2-thiolases (type-1, type-2) are classified as CHH-thiolases, having as corresponding fingerprints xS, DCF and G P. In all thiolases, OAH2 is formed by the main chain NH groups of two catalytic loops. In the well-studied CNH-thiolases, OAH1 is formed by a water (of the Wat-Asn(NEAF) dyad) and NE2 (of the GHP-histidine). In the two described liganded Lm-thiolase structures, it is seen that in this CHH-thiolase, OAH1 is formed by NE2 of His338 (HDCF) and His388 (GHP). Analysis of the OAH1 hydrogen bond networks suggests that the GHP-histidine is doubly protonated and positively charged in these complexes, whereas the HDCF histidine is neutral and singly protonated.

  • Organizational Affiliation

    Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), UMR5234, Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076 Bordeaux, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-ketoacyl-CoA thiolase-like protein
A, B, C, D
457Leishmania mexicana MHOM/GT/2001/U1103Mutation(s): 0 
Gene Names: LMXM_23_0690
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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.701α = 90
b = 89.889β = 105.78
c = 126.332γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Academy of FinlandFinland131795
European Commissions Seventh FrameworkFinlandFP7/2007-2013

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references