2QEY

Rat cytosolic PEPCK in complex with GTP

2QEY の概要

• エントリーDOI: 10.2210/pdb2qey/pdb
• 関連するPDBエントリー: 2QEW 2QF1 2QF2
• 分子名称: Phosphoenolpyruvate carboxykinase, cytosolic [GTP], MANGANESE (II) ION, SODIUM ION, ... (6 entities in total)
• 機能のキーワード: pepck, phosphoenolpyruvate carboxykinase, gluconeogenesis, gtp, kinase, lyase
• 由来する生物種: Rattus norvegicus (Norway rat)
• 細胞内の位置: Cytoplasm: P07379
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 70416.84

構造登録者

Sullivan, S.M.,Holyoak, T. (登録日: 2007-06-26, 公開日: 2007-08-21, 最終更新日: 2023-08-30)

主引用文献

Sullivan, S.M.,Holyoak, T.
Structures of rat cytosolic PEPCK: insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid.
Biochemistry, 46:10078-10088, 2007

PubMed Abstract: The structures of the rat cytosolic isoform of phosphoenolpyruvate carboxykinase (PEPCK) reported in the PEPCK-Mn2+, -Mn2+-oxaloacetic acid (OAA), -Mn2+-OAA-Mn2+-guanosine-5'-diphosphate (GDP), and -Mn2+-Mn2+-guanosine-5'-tri-phosphate (GTP) complexes provide insight into the mechanism of phosphoryl transfer and decarboxylation mediated by this enzyme. OAA is observed to bind in a number of different orientations coordinating directly to the active site metal. The Mn2+-OAA and Mn2+-OAA-Mn2+GDP structures illustrate inner-sphere coordination of OAA to the manganese ion through the displacement of two of the three water molecules coordinated to the metal in the holo-enzyme by the C3 and C4 carbonyl oxygens. In the PEPCK-Mn2+-OAA complex, an alternate bound conformation of OAA is present. In this conformation, in addition to the previous interactions, the C1 carboxylate is directly coordinated to the active site Mn2+, displacing all of the waters coordinated to the metal in the holo-enzyme. In the PEPCK-Mn2+-GTP structure, the same water molecule displaced by the C1 carboxylate of OAA is displaced by one of the gamma-phosphate oxygens of the triphosphate nucleotide. The structures are consistent with a mechanism of direct in-line phosphoryl transfer, supported by the observed stereochemistry of the reaction. In the catalytically competent binding mode, the C1 carboxylate of OAA is sandwiched between R87 and R405 in an environment that would serve to facilitate decarboxylation. In the reverse reaction, these two arginines would form the CO2 binding site. Comparison of the Mn2+-OAA-Mn2+GDP and Mn2+-Mn2+GTP structures illustrates a marked difference in the bound conformations of the nucleotide substrates in which the GTP nucleotide is bound in a high-energy state resulting from the eclipsing of all three of the phosphoryl groups along the triphosphate chain. This contrasts a previously determined structure of PEPCK in complex with a triphosphate nucleotide analogue in which the analogue mirrors the conformation of GDP as opposed to GTP. Last, the structures illustrate a correlation between conformational changes in the P-loop, the nucleotide binding site, and the active site lid that are important for catalysis.

PubMed: 17685635
DOI: 10.1021/bi701038x

実験手法

X-RAY DIFFRACTION (1.9 Å)