5V9F

Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruvate and GTP.

  • Classification: LYASE
  • Organism(s): Rattus norvegicus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2017-03-23 Released: 2017-04-12 
  • Deposition Author(s): Holyoak, T., Cui, D.S.
  • Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.4 of the entry. See complete history. 


Literature

Asymmetric Anchoring Is Required for Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase.

Cui, D.S., Broom, A., Mcleod, M.J., Meiering, E.M., Holyoak, T.

(2017) Biochemistry 56: 2106-2115

  • DOI: 10.1021/acs.biochem.7b00178
  • Primary Citation of Related Structures:  
    5V95, 5V97, 5V9F, 5V9G, 5V9H

  • PubMed Abstract: 

    • Mobile Ω-loops play essential roles in the function of many enzymes. Here we investigated the importance of a residue lying outside of the mobile Ω-loop element in the catalytic function of an H477R variant of cytosolic phosphoenolpyruvate carboxykinase using crystallographic, kinetic, and computational analysis ...

    Mobile Ω-loops play essential roles in the function of many enzymes. Here we investigated the importance of a residue lying outside of the mobile Ω-loop element in the catalytic function of an H477R variant of cytosolic phosphoenolpyruvate carboxykinase using crystallographic, kinetic, and computational analysis. The crystallographic data suggest that the efficient transition of the Ω-loop to the closed conformation requires stabilization of the N-terminus of the loop through contacts between R461 and E588. In contrast, the C-terminal end of the Ω-loop undergoes changing interactions with the enzyme body through contacts between H477 at the C-terminus of the loop and E591 located on the enzyme body. Potential of mean force calculations demonstrated that altering the anchoring of the C-terminus of the Ω-loop via the H477R substitution results in the destabilization of the closed state of the Ω-loop by 3.4 kcal mol -1 . The kinetic parameters for the enzyme were altered in an asymmetric fashion with the predominant effect being observed in the direction of oxaloacetate synthesis. This is exemplified by a reduction in k cat for the H477R mutant by an order of magnitude in the direction of OAA synthesis, while in the direction of PEP synthesis, it decreased by a factor of only 2. The data are consistent with a mechanism for loop conformational exchange between open and closed states in which a balance between fixed anchoring of the N-terminus of the Ω-loop and a flexible, unattached C-terminus drives the transition between a disordered (open) state and an ordered (closed) state.

    Organizational Affiliation: 

    Department of Biology and ‡Department of Chemistry, University of Waterloo , Waterloo, ON, Canada N2L 3G1.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]A622Rattus norvegicusMutation(s): 1 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
SPV
Query on SPV
Download Ideal Coordinates CCD File 
F [auth A]SULFOPYRUVATE
C3 H4 O6 S
BUTHMSUEBYPMKJ-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
G [auth A]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SPV BindingDB:  5V9F Ki: 3.70e+4 (nM) from 1 assay(s)
Binding MOAD:  5V9F Ki: 3.70e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.285α = 90
b = 119.506β = 107.81
c = 60.707γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-23 
  • Released Date: 2017-04-12 
    • Deposition Author(s): Holyoak, T., Cui, D.S.
Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2017-09-27
    Changes: Data collection
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence