9e38 | pdb_00009e38
Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with phosphoglycolic acid and GDP
Structural highlights
FunctionA1VIE9_POLNA Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP), the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle.[HAMAP-Rule:MF_00452] Publication Abstract from PubMedTemperature is a critical factor in enzyme function, as most enzymes are thermally activated. Across Earth's diverse environments (-20 to 120 degrees C), enzymes have evolved to function optimally at their organism's growth temperature. Thermophilic enzymes must resist denaturation, while psychrophilic enzymes must maintain activity with limited thermal energy. Although principles underlying thermostability are well established, the mechanisms governing kinetic adaptation to temperature remain less understood. To investigate this, we characterized the kinetics and determined a comprehensive series of X-ray crystal structures of a psychrophilic, GTP-dependent phosphoenolpyruvate carboxykinase (PEPCK) bound to substrates and non-reactive mimics of the reaction coordinate. These structures were compared to those of a mesophilic PEPCK. PEPCK is a dynamic enzyme requiring substantial conformational changes during catalysis, particularly ordering of the active site Omega-loop lid. The psychrophilic enzyme exhibited a reduced catalytic efficiency (k(cat)/K(M)) and lower optimal temperature (T(opt)) relative to its mesophilic counterpart. Structural comparisons revealed substitutions in the Omega-loop that likely increase the entropic cost of loop ordering and reduce enthalpic stabilization, hindering efficient active site closure. These results provide a mechanistic basis for cold adaptation in enzyme catalysis, linking specific structural features to altered kinetic behavior. Understanding such adaptations not only advances our knowledge of enzyme evolution but also informs protein engineering efforts aimed at designing efficient biocatalysts for industrial applications operating at non-physiological temperatures. Structural mechanisms for cold-adapted activity of phosphoenolpyruvate carboxykinase.,McLeod MJ, Yazdani S, Barwell SAE, Holyoak T Protein Sci. 2025 Nov;34(11):e70326. doi: 10.1002/pro.70326. PMID:41099612[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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