3N25

The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The pyruvate kinase model system, a cautionary tale for the use of osmolyte perturbations to support conformational equilibria in allostery.

Fenton, A.W.Johnson, T.A.Holyoak, T.

(2010) Protein Sci. 19: 1796-1800

  • DOI: 10.1002/pro.450

  • PubMed Abstract: 
  • In the study of rabbit muscle pyruvate kinase (M1-PYK), proline has previously been used as an osmolyte in an attempt to determine a role for preexisting conformational equilibria in allosteric regulation. In this context, osmolytes are small molecul ...

    In the study of rabbit muscle pyruvate kinase (M1-PYK), proline has previously been used as an osmolyte in an attempt to determine a role for preexisting conformational equilibria in allosteric regulation. In this context, osmolytes are small molecules assumed to have no direct interaction with the protein. In contrast to proline's proposed role as an osmolyte, the structure of M1PYK-Mn-pyruvate-proline complex reported herein demonstrates that proline binds specifically to the allosteric site of M1-PYK. Therefore, this amino acid is an allosteric effector rather than a benign osmolyte. Other compounds often used as osmolytes (polyethyleneglycol and glycerol) are also present in the structure, suggesting an interaction with the protein that would, in turn, prevent the usefulness of these compounds in the study of this and most likely other proteins. These findings highlight the need to verify that compounds used as osmolytes to perturb preexisting conformational equilibrium do not directly interact with the protein, a consideration not commonly addressed in the past.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160, USA. afenton@kumc.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase isozymes M1/M2
A, B, C, D, E, F, G, H
531Oryctolagus cuniculusMutation(s): 0 
Gene Names: PKM (PKM2)
EC: 2.7.1.40
Find proteins for P11974 (Oryctolagus cuniculus)
Go to Gene View: PKM
Go to UniProtKB:  P11974
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B, C, D, E, F, G, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A, B, C, D, E, F, G, H
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, C, D, E, F, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PYR
Query on PYR

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Download CCD File 
A, B, C, D, E, F, G, H
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C, D, E, F, H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PRO
Query on PRO

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Download CCD File 
A, B, C, D, E, F, G, H
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 82.373α = 95.18
b = 108.747β = 93.38
c = 144.256γ = 112.23
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description
  • Version 1.3: 2018-04-04
    Type: Data collection