8E1U

Propionibacterium freudenreichii PPi-dependent PEPCK in complex with malate

Summary for 8E1U

• Entry DOI: 10.2210/pdb8e1u/pdb
• Descriptor: PPi-dependent PEPCK, MAGNESIUM ION, D-MALATE, ... (4 entities in total)
• Functional Keywords: allosteric inhibitor, lyase
• Biological source: Propionibacterium freudenreichii subsp. shermanii
• Total number of polymer chains: 8
• Total formula weight: 1019171.46

Authors

McLeod, M.J.,Holyoak, T. (deposition date: 2022-08-11, release date: 2023-06-07, Last modification date: 2023-10-25)

Primary citation

McLeod, M.J.,Holyoak, T.
Biochemical, structural, and kinetic characterization of PP i -dependent phosphoenolpyruvate carboxykinase from Propionibacterium freudenreichii.
Proteins, 91:1261-1275, 2023

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 -PfPEPCK), which instead of using a nucleotide, utilized PP to catalyze the same interconversion of OAA and PEP. The presented work expands upon the initial biochemical experiments for PP -PfPEPCK and interprets these data considering both the current understanding of nucleotide-dependent PEPCKs and is supplemented with a new crystal structure of PP -PfPEPCK in complex with malate at a putative allosteric site. Most interesting, the data are consistent with PP -PfPEPCK being a Fe activated enzyme in contrast with the Mn 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.

PubMed: 37226637
DOI: 10.1002/prot.26513

Experimental method

X-RAY DIFFRACTION (2.65 Å)