4KS0

Pyruvate kinase (PYK) from Trypanosoma cruzi in the presence of Magnesium, oxalate and F26BP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of pyruvate kinases display evolutionarily divergent allosteric strategies.

Morgan, H.P.Zhong, W.McNae, I.W.Michels, P.A.Fothergill-Gilmore, L.A.Walkinshaw, M.D.

(2014) R Soc Open Sci 1: 140120-140120

  • DOI: 10.1098/rsos.140120
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the fou ...

    The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (k cat/S 0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (k cat/S 0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors.


    Organizational Affiliation

    Centre for Translational and Chemical Biology, School of Biological Sciences , University of Edinburgh , Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase
A, B
519Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
EC: 2.7.1.40
Find proteins for Q4D9Z4 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4D9Z4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
FDP
Query on FDP

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Download CCD File 
A, B
FRUCTOSE-2,6-DIPHOSPHATE
C6 H14 O12 P2
YXWOAJXNVLXPMU-ZXXMMSQZSA-N
 Ligand Interaction
OXL
Query on OXL

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Download CCD File 
A, B
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 173.767α = 90.00
b = 173.767β = 90.00
c = 211.855γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references