3HQP

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The allosteric mechanism of pryuvate kinase from Leishmania mexicana: a rock and lock model

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

(2010) J.Biol.Chem. 285: 12892-12898

  • DOI: 10.1074/jbc.M109.079905
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Allosteric regulation provides a rate management system for enzymes involved in many cellular processes. Ligand-controlled regulation is easily recognizable, but the underlying molecular mechanisms have remained elusive. We have obtained the first co ...

    Allosteric regulation provides a rate management system for enzymes involved in many cellular processes. Ligand-controlled regulation is easily recognizable, but the underlying molecular mechanisms have remained elusive. We have obtained the first complete series of allosteric structures, in all possible ligated states, for the tetrameric enzyme, pyruvate kinase, from Leishmania mexicana. The transition between inactive T-state and active R-state is accompanied by a simple symmetrical 6 degrees rigid body rocking motion of the A- and C-domain cores in each of the four subunits. However, formation of the R-state in this way is only part of the mechanism; eight essential salt bridge locks that form across the C-C interface provide tetramer rigidity with a coupled 7-fold increase in rate. The results presented here illustrate how conformational changes coupled with effector binding correlate with loss of flexibility and increase in thermal stability providing a general mechanism for allosteric control.


    Organizational Affiliation

    Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
499Leishmania mexicanaMutation(s): 0 
Gene Names: PYK
EC: 2.7.1.40
Find proteins for Q27686 (Leishmania mexicana)
Go to UniProtKB:  Q27686
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ATP
Query on ATP

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, P
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
FDP
Query on FDP

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
FRUCTOSE-2,6-DIPHOSPHATE
C6 H14 O12 P2
YXWOAJXNVLXPMU-ZXXMMSQZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
E, G, I, J, O
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
OXL
Query on OXL

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, P
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 127.486α = 89.73
b = 151.140β = 80.17
c = 160.319γ = 71.64
Software Package:
Software NamePurpose
DNAdata collection
REFMACrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance