Propionibacterium freudenreichii PPi-dependent PEPCK in complex with malate

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Biochemical, structural, and kinetic characterization of PP i -dependent phosphoenolpyruvate carboxykinase from Propionibacterium freudenreichii.

McLeod, M.J.Holyoak, T.

(2023) Proteins 91: 1261-1275

  • DOI: https://doi.org/10.1002/prot.26513
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Phosphoenolpyruvate carboxykinases (PEPCK) are a well-studied family of enzymes responsible for the regulation of TCA cycle flux, where they catalyze the interconversion of oxaloacetic acid (OAA) and phosphoenolpyruvate (PEP) using a phosphoryl donor/acceptor. These enzymes have typically been divided into two nucleotide-dependent classes, those that use ATP and those that use GTP. In the 1960's and early 1970's, a group of papers detailed biochemical properties of an enzyme named phosphoenolpyruvate carboxytransphosphorylase (later identified as a third PEPCK) from Propionibacterium freudenreichii (PP i -PfPEPCK), which instead of using a nucleotide, utilized PP i to catalyze the same interconversion of OAA and PEP. The presented work expands upon the initial biochemical experiments for PP i -PfPEPCK and interprets these data considering both the current understanding of nucleotide-dependent PEPCKs and is supplemented with a new crystal structure of PP i -PfPEPCK in complex with malate at a putative allosteric site. Most interesting, the data are consistent with PP i -PfPEPCK being a Fe 2+ activated enzyme in contrast with the Mn 2+ activated nucleotide-dependent enzymes which in part results in some unique kinetic properties for the enzyme when compared to the more widely distributed GTP- and ATP-dependent enzymes.

  • Organizational Affiliation

    Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PPi-dependent PEPCK
A, B, C, D, E
A, B, C, D, E, F, G, H
1,131Propionibacterium freudenreichii subsp. shermaniiMutation(s): 0 
Gene Names: PFREUDJS001_000139
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLT (Subject of Investigation/LOI)
Query on MLT

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
R [auth F]
T [auth G]
J [auth A],
L [auth B],
N [auth C],
R [auth F],
T [auth G],
V [auth H]
C4 H6 O5
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
P [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
P [auth E],
Q [auth F],
S [auth G],
U [auth H]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.131α = 82.7
b = 146.952β = 84
c = 151.094γ = 70.8
Software Package:
Software NamePurpose
DIALSdata reduction
DIALSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Refinement description