2RK8

The Structure of rat cytosolic PEPCK in complex with phosphonoformate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Differential Inhibition of Cytosolic PEPCK by Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition.

Stiffin, R.M.Sullivan, S.M.Carlson, G.M.Holyoak, T.

(2008) Biochemistry 47: 2099-2109

  • DOI: 10.1021/bi7020662
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mechanisms of molecular recognition of phosphoenolpyruvate (PEP) and oxaloacetate (OAA) by cytosolic phosphoenolpyruvate carboxykinase (cPEPCK) were investigated by the systematic evaluation of a variety of PEP and OAA analogues as potential reve ...

    The mechanisms of molecular recognition of phosphoenolpyruvate (PEP) and oxaloacetate (OAA) by cytosolic phosphoenolpyruvate carboxykinase (cPEPCK) were investigated by the systematic evaluation of a variety of PEP and OAA analogues as potential reversible inhibitors of the enzyme against PEP. The molecules that inhibit the enzyme in a competitive fashion were found to fall into two general classes. Those molecules that mimic the binding geometry of PEP, namely phosphoglycolate and 3-phosphonopropionate, are found to bind weakly (millimolar Ki values). In contrast, those competitive inhibitors that mimic the binding of OAA (oxalate and phosphonoformate) coordinate directly to the active site manganese ion and bind an order of magnitude more tightly (micromolar Ki values). The competitive inhibitor sulfoacetate is found to be an outlier of these two classes, binding in a hybrid fashion utilizing modes of recognition of both PEP and OAA in order to achieve a micromolar inhibition constant in the absence of direct coordination to the active site metal. The kinetic studies in combination with the structural characterization of the five aforementioned competitive inhibitors demonstrate the molecular requirements for high affinity binding of molecules to the active site of the enzyme. These features include cis-planar carbonyl groups that are required for coordination to the active site metal, a bridging electron rich atom at the position corresponding to the C2 methylene group of OAA to facilitate interactions with R405, a carboxylate or sulfonate moiety at a position corresponding to the C1 carboxylate of OAA, and the edge-on aromatic interaction between a carboxylate and Y235.


    Organizational Affiliation

    Department of Molecular Biosciences, The University of Tennessee Health Science Center, Memphis, Tennessee 38163, 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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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
FMT
Query on FMT

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A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
PPF
Query on PPF

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A, B
PHOSPHONOFORMIC ACID
C H3 O5 P
ZJAOAACCNHFJAH-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PPFKi: 230000 nM BINDINGMOAD
PPFKi: 230000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.251α = 90.00
b = 119.470β = 107.06
c = 86.870γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
CrystalCleardata collection
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description