Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 436511.97 
• Atom Count: 30034 
• Residue Count: 3992 
• Unique protein chains: 1

1PKL

THE STRUCTURE OF LEISHMANIA PYRUVATE KINASE

• DOI: 10.2210/pdb1PKL/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania mexicana
• Expression System: Escherichia coli


• Deposited: 1998-09-15 Released: 1998-09-23 
• Deposition Author(s): Rigden, D.J., Phillips, S.E.V., Michels, P.A.M., Fothergill-Gilmore, L.A.

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Experimental Data Snapshot

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

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

• PubMed: 10448041 
• DOI: 10.1006/jmbi.1999.2918


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (PYRUVATE KINASE)	A, B, C, D, E, F, H, G	499	Leishmania mexicana	Mutation(s): 0  Gene Names: PYK EC: 2.7.1.40
Find proteins for Q27686 (Leishmania mexicana) Go to UniProtKB:  Q27686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C, D, E, F, G, H	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.256 
• R-Value Work: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 121.649	α = 90.00
b = 132.638	β = 97.11
c = 180.996	γ = 90.00

Software Package:

Software Name	Purpose
MLPHARE	phasing
CCP4	data scaling
DM	phasing
DENZO	data reduction
X-PLOR	refinement
DM	model building
FFT	phasing
SHELXS	phasing
FFT	model building
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-09-15 
• Released Date: 1998-09-23 
• Deposition Author(s): Rigden, D.J., Phillips, S.E.V., Michels, P.A.M., Fothergill-Gilmore, L.A.

Revision History 

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