1PKL

THE STRUCTURE OF LEISHMANIA PYRUVATE KINASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The structure of pyruvate kinase from Leishmania mexicana reveals details of the allosteric transition and unusual effector specificity.

Rigden, D.J., Phillips, S.E., Michels, P.A., Fothergill-Gilmore, L.A.

(1999) J Mol Biol 291: 615-635

  • DOI: 10.1006/jmbi.1999.2918
  • Primary Citation of Related Structures:  
    1PKL

  • PubMed Abstract: 

    • Glycolysis occupies a central role in cellular metabolism, and is of particular importance for the catabolic production of ATP in protozoan parasites such as Leishmania and Trypanosoma. In these organisms pyruvate kinase plays a key regulatory role, and is unique in responding to fructose 2,6-bisphosphate as allosteric activator ...

    Glycolysis occupies a central role in cellular metabolism, and is of particular importance for the catabolic production of ATP in protozoan parasites such as Leishmania and Trypanosoma. In these organisms pyruvate kinase plays a key regulatory role, and is unique in responding to fructose 2,6-bisphosphate as allosteric activator. The determination of the first eukaryotic pyruvate kinase crystal structure in the T-state is reported. A comparison of the leishmania and yeast R-state enzymes reveals fewer differences than the previous comparison of Escherichia coli T-state and rabbit muscle non-allosteric enzymes. Structural changes related to the allosteric transition can therefore be distinguished from those that are a consequence of the inherent wide structural divergence between bacterial and mammalian proteins. The allosteric transition involves significant changes in a tightly packed array of eight alpha helices at the interface near the catalytic site. At the other interface the allosteric transition appears to be accompanied by the bending of a ten-stranded intersubunit beta sheet adjacent to the effector site. Helix Calpha1 makes contacts to the N-terminal helical domain and bridges both interfaces. A comparison of the effector sites of the leishmania and yeast enzymes reveals the structural basis for the different effector specificity. Two loops comprising residues 443-453 and 480-489 adopt very different conformations in the two enzymes, and Lys453 and His480 that are a feature of trypanosomatid enzymes provide probable ligands for the 2-phospho group of the effector molecule. These differences offer an opportunity for the design of drugs that would bind to the trypanosomatid enzymes but not to those of the mammalian host.

    Organizational Affiliation: 

    School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, England.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PYRUVATE KINASE)
A,
B,
C,
D,
E,
499Leishmania mexicanaMutation(s): 0 
Gene Names: PYK
EC: 2.7.1.40
UniProt
Find proteins for Q27686 (Leishmania mexicana)
Explore Q27686 
Go to UniProtKB:  Q27686
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ27686
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.649α = 90
b = 132.638β = 97.11
c = 180.996γ = 90
Software Package:
Software NamePurpose
AMoREphasing
FFTmodel building
SHELXSphasing
MLPHAREphasing
DMmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
FFTphasing
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-23
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance