3DTB

The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection.

Sullivan, S.M.Holyoak, T.

(2008) Proc.Natl.Acad.Sci.Usa 105: 13829-13834

  • DOI: 10.1073/pnas.0805364105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligat ...

    The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics and catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
A, B
624Rattus norvegicusMutation(s): 0 
Gene Names: Pck1
EC: 4.1.1.32
Find proteins for P07379 (Rattus norvegicus)
Go to UniProtKB:  P07379
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
EPE
Query on EPE

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Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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Download CCD File 
A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
PGA
Query on PGA

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Download CCD File 
A, B
2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.154α = 90.00
b = 119.683β = 107.05
c = 86.849γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
HKL-2000data reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description