4UXX

Structure of delta4-DgkA with AMPPCP in 9.9 MAG

4UXX の概要

• エントリーDOI: 10.2210/pdb4uxx/pdb
• 関連するPDBエントリー: 4UXW 4UXZ
• 分子名称: DIACYLGLYCEROL KINASE, CHLORIDE ION, SODIUM ION, ... (9 entities in total)
• 機能のキーワード: transferase, atp analogue, dgka, diacylglyerol kinase, in meso crystallization, lipid cubic phase, lipidic cubic phase, lipid mesophase, lipidic mesophase, membrane protein, 9.9 mag, monoacylglycerol, non- hydrolyzable atp analogue, nucleotide analogue
• 由来する生物種: ESCHERICHIA COLI K-12
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 45896.58

構造登録者

Li, D.,Vogeley, L.,Caffrey, M. (登録日: 2014-08-27, 公開日: 2015-09-30, 最終更新日: 2024-01-10)

主引用文献

Li, D.,Stansfeld, P.J.,Sansom, M.S.P.,Keogh, A.,Vogeley, L.,Howe, N.,Lyons, J.A.,Aragao, D.,Fromme, P.,Fromme, R.,Basu, S.,Grotjohann, I.,Kupitz, C.,Rendek, K.,Weierstall, U.,Zatsepin, N.A.,Cherezov, V.,Liu, W.,Bandaru, S.,English, N.J.,Gati, C.,Barty, A.,Yefanov, O.,Chapman, H.N.,Diederichs, K.,Messerschmidt, M.,Boutet, S.,Williams, G.J.,Marvin Seibert, M.,Caffrey, M.
Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase.
Nat.Commun., 6:10140-, 2015

PubMed Abstract: Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.

PubMed: 26673816
DOI: 10.1038/NCOMMS10140

実験手法

X-RAY DIFFRACTION (2.701 Å)