4YWB

Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid and oxalic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Inhibition and Allosteric Regulation of Monomeric Phosphoenolpyruvate Carboxykinase by 3-Mercaptopicolinic Acid.

Balan, M.D.Mcleod, M.J.Lotosky, W.R.Ghaly, M.Holyoak, T.

(2015) Biochemistry 54: 5878-5887

  • DOI: 10.1021/acs.biochem.5b00822
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For almost 40 years, it has been known that tryptophan metabolites and picolinic acid analogues act as inhibitors of gluconeogenesis. Early studies observed that 3-mercaptopicolinic acid (MPA) was a potent hypoglycemic agent via inhibition of glucose ...

    For almost 40 years, it has been known that tryptophan metabolites and picolinic acid analogues act as inhibitors of gluconeogenesis. Early studies observed that 3-mercaptopicolinic acid (MPA) was a potent hypoglycemic agent via inhibition of glucose synthesis through the specific inhibition of phosphoenolpyruvate carboxykinase (PEPCK) in the gluconeogenesis pathway. Despite prior kinetic investigation, the mechanism of the inhibition by MPA is unclear. To clarify the mechanism of inhibition exerted by MPA on PEPCK, we have undertaken structural and kinetic studies. The kinetic data in concert with crystallographic structures of PEPCK in complex with MPA and the substrates for the reaction illustrate that PEPCK is inhibited by the binding of MPA at two discrete binding sites: one acting in a competitive fashion with PEP/OAA (∼10 μM) and the other acting at a previously unidentified allosteric site (Ki ∼ 150 μM). The structural studies suggest that binding of MPA to the allosteric pocket stabilizes an altered conformation of the nucleotide-binding site that in turn reduces the affinity of the enzyme for the nucleotide.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center , Kansas City, Kansas 66160, United States.,Department of Biology, University of Waterloo , Waterloo, ON N2L 3G1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
A, C
622Rattus norvegicusMutation(s): 0 
Gene Names: Pck1
EC: 4.1.1.32
Find proteins for P07379 (Rattus norvegicus)
Go to UniProtKB:  P07379
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
OXD
Query on OXD

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A, C
OXALIC ACID
C2 H2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
1WD
Query on 1WD

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A, C
3-sulfanylpyridine-2-carboxylic acid
C6 H5 N O2 S
ZYFDNIOIEFZULT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1WDKi: 37000 - 180000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.124α = 90.00
b = 118.732β = 107.27
c = 86.393γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesP20RR17708
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references
  • Version 1.2: 2016-06-08
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Type: Author supporting evidence