1A5U
PYRUVATE KINASE COMPLEX WITH BIS MG-ATP-NA-OXALATE
1A5U の概要
エントリーDOI | 10.2210/pdb1a5u/pdb |
分子名称 | PYRUVATE KINASE, SODIUM ION, OXALATE ION, ... (6 entities in total) |
機能のキーワード | pyruvate kinase, transferase |
由来する生物種 | Oryctolagus cuniculus (rabbit) |
細胞内の位置 | Cytoplasm : P11974 |
タンパク質・核酸の鎖数 | 8 |
化学式量合計 | 468261.99 |
構造登録者 | Larsen, T.M.,Benning, M.M.,Rayment, I.,Reed, G.H. (登録日: 1998-02-18, 公開日: 1999-03-02, 最終更新日: 2024-05-22) |
主引用文献 | Larsen, T.M.,Benning, M.M.,Rayment, I.,Reed, G.H. Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel. Biochemistry, 37:6247-6255, 1998 Cited by PubMed Abstract: Pyruvate kinase from rabbit muscle has been cocrystallized as a complex with MgIIATP, oxalate, Mg2+, and either K+ or Na+. Crystals with either Na+ or K+ belong to the space group P2(1)2(1)2(1), and the asymmetric units contain two tetramers. The structures were solved by molecular replacement and refined to 2.1 (K+) and 2.35 A (Na+) resolution. The structures of the Na+ and K+ complexes are virtually isomorphous. Each of the eight subunits within the asymmetric unit contains MgIIoxalate as a bidentate complex linked to the protein through coordination of Mg2+ to the carboxylates of Glu 271 and Asp 295. Six of the subunits also contain an alpha,beta,gamma-tridentate complex of MgIIATP, and the active-site cleft, located between domains A and B, is closed in these subunits. In the remaining two subunits MgIIATP is missing, and the active-site cleft is open. Closure of the active-site cleft in the fully liganded subunits includes a rotation of 41 degrees of the B domain relative to the A domain. alpha-Carbons of residues in the B domain undergo movements of up to 17.8 A (Lys 124) in the cleft closure. Lys 206, Arg 119, and Asp 177 from the B domain move several angstroms from their positions in the open conformation to contact the MgIIATP complex in the active site. The gamma-phosphate of ATP coordinates to both magnesium ions and to the monovalent cation, K+ or Na+. A Mg2+-coordinated oxygen from the MgIIoxalate complex lies 3.0 A from Pgamma of ATP, and this oxygen is positioned for an in-line attack on the phosphorus. The side chains of Lys 269 and Arg 119 are positioned to provide leaving-group activation in the forward and reverse directions. There is no obvious candidate for the acid/base catalyst near the 2-si face of the prospective enolate of the normal substrate. A functional group linked through solvent and side-chain hydroxyls may function in a proton relay. PubMed: 9572839DOI: 10.1021/bi980243s 主引用文献が同じPDBエントリー |
実験手法 | X-RAY DIFFRACTION (2.35 Å) |
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