6ASM

E. coli phosphoenolpyruvate carboxykinase G209S K212C mutant bound to thiosulfate

6ASM の概要

• エントリーDOI: 10.2210/pdb6asm/pdb
• 分子名称: Phosphoenolpyruvate carboxykinase (ATP), ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (8 entities in total)
• 機能のキーワード: nonnative ligand, lyase
• 由来する生物種: Escherichia coli (strain K12)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 61581.14

構造登録者

Tang, H.Y.H.,Shin, D.S.,Tainer, J.A. (登録日: 2017-08-25, 公開日: 2018-08-29, 最終更新日: 2024-03-13)

主引用文献

Tang, H.Y.H.,Shin, D.S.,Hura, G.L.,Yang, Y.,Hu, X.,Lightstone, F.C.,McGee, M.D.,Padgett, H.S.,Yannone, S.M.,Tainer, J.A.
Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase.
Biochemistry, 57:6688-6700, 2018

PubMed Abstract: Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, critical features of ligand binding, position, and metal ion cofactor geometry required for all downstream events can be engineered with small numbers of mutations to provide insights into fundamental underpinnings of protein-ligand recognition. Through structural and computational knowledge, the combination of designed and random mutations aids in the robust design of predetermined changes to ligand binding and activity to engineer protein function.

PubMed: 30376300
DOI: 10.1021/acs.biochem.8b00963

実験手法

X-RAY DIFFRACTION (1.55 Å)