4KS0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1098/rsos.140120
  • Primary Citation of Related Structures:  
    4KRZ, 4KS0

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase
A, B
519Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: Tc00.1047053511281.60
EC: 2.7.1.40
UniProt
Find proteins for Q4D9Z4 (Trypanosoma cruzi (strain CL Brener))
Explore Q4D9Z4 
Go to UniProtKB:  Q4D9Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4D9Z4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDP
Query on FDP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
2,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
YXWOAJXNVLXPMU-ZXXMMSQZSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.767α = 90
b = 173.767β = 90
c = 211.855γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Structure summary