Ferguson, Scarlett Blair (2012-10). Understanding Weak Binding for Phospho(enol)pyruvate to the Allosteric Site of Phosphofructokinase from Lactobacillus delbrueckii subspecies bulgaricus. Doctoral Dissertation.
Thesis
Phosphofructokinase (PFK) from the lactic acid bacterium Lactobacillus delbrueckii subspecies bulgaricus (LbPFK) is a non-allosteric PFK with weak binding affinity for both the allosteric ligands phospho(enol)pyruvate (PEP) and magnesium adenosine diphosphate (MgADP). PEP and MgADP bind to the same allosteric binding site but exhibit opposite effects, PEP acting as an inhibitor and MgADP an activator. In 2005, Parichatttanakul, et al. solved the first crystal structure of LbPFK to 1.87 A resolution and allowed for a structural comparison of LbPFK to the allosteric forms of PFK from E. coli (EcPFK) and Bacillus stearothermophilus (BsPFK). Two additional structures of LbPFK have been determined with the first having phosphates bound at the four active sites and four allosteric sites solved to 2.20 A resolution. The second structure solved to 1.83 A resolution contains phosphates at all eight sites with the addition of the substrate fructose-6-phosphate (F6P) in the active sites. These structures are similar to the published sulfate-bound LbPFK structure. Overall, the secondary, tertiary and quaternary structure is conserved with the exception of the residues in the allosteric site. E55, H59, S211, D214, H215 and G216, as well as the long cassettes of residues 52-61 (PFKs1) and 206-218 (PFKs2) were mutated to the corresponding residue/residues in Thermus thermophilus PFK (TtPFK). PFKs1 and PFKs1 were also combined to form PFKs1s2. The single mutations along with PFKs1 and PFKs2 showed no enhancement in PEP binding, but PFKs1s2 enhanced PEP binding 10-fold with no change in MgADP binding compared to LbPFK. D12, located along the active site interface 15 A away from the allosteric site, was mutated to an alanine and exhibited enhanced binding 9-fold for both PEP and MgADP to the allosteric binding site. A crystal structure of D12A was solved to 2.30 A resolution with sulfate bound to all eight binding sites, and showed no major changes in secondary, tertiary or quaternary structure when compared to the sulfate-bound wild-type LbPFK structure. Combining D12A with PFKs1s2 (PFKs1s2/D12A) further enhanced PEP binding with a 21-fold tighter binding compared to LbPFK with MgADP binding being similar to D12A. PEP inhibition was also quantitated in PFKs1s2/D12A with a Q_ay = 0.007 plus/minus 0.0008. Coupling between PEP and F6P in PFKs1s2D12A is 2-fold stronger than the coupling measured in EcPFK and 7-fold stronger than the coupling measured in BsPFK. The coupling measured in PFKs1s2D12A is the first measured in any of the LbPFK variants.
