9EIY | pdb_00009eiy

Rat cytosolic PEPCK in complex with GDP and phosphoglycolic acid (313K)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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Literature

A structural perspective on the temperature dependent activity of enzymes.

McLeod, M.J.Barwell, S.A.E.Holyoak, T.Thorne, R.E.

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.02.013
  • Primary Citation of Related Structures:  
    9EIV, 9EIW, 9EIX, 9EIY, 9EIZ, 9EJ0, 9EJ1, 9EJ2, 9EJ3, 9EJ4, 9EJ5, 9EJ6

  • PubMed Abstract: 

    Enzyme activity varies with temperature. Unlike small-molecule catalysts, the structural ensembles of enzymes can change substantially with temperature, but it is unclear how this modulates temperature dependent activity. Here, multi-temperature X-ray crystallography was used to record structural changes from -20°C to 40°C for a mesophilic enzyme in complex with inhibitors mimicking substrate-, intermediate-, and product-bound states, representative of major complexes on the reaction coordinate. Inhibitors, substrates and active site loops increasingly populated catalytically competent conformations as temperature increased. These changes occurred even in temperature ranges where kinetic measurements showed roughly linear Arrhenius/Eyring behavior, where parameters characterizing the system are assumed to be temperature independent. Simple analysis shows that linear Arrhenius/Eyring behavior can still be observed when the underlying activation energy/enthalpy values vary with temperature. Our results indicate a critical role for temperature dependent atomic-resolution structural data in interpreting temperature dependent kinetic data from enzymatic systems.


  • Organizational Affiliation

    Cornell University, Department of Physics, Ithaca, NY 14850, USA; University of Waterloo, Department of Biology, Waterloo ON N2L 3G1, Canada. Electronic address: mjm758@cornell.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]622Rattus norvegicusMutation(s): 0 
Gene Names: Pck1
EC: 4.1.1.32 (PDB Primary Data), 2.7.11 (UniProt)
UniProt
Find proteins for P07379 (Rattus norvegicus)
Explore P07379 
Go to UniProtKB:  P07379
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07379
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.892α = 90
b = 120.165β = 110.19
c = 61.407γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDBI-2210041
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM127528-02

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release