4UXX

Structure of delta4-DgkA with AMPPCP in 9.9 MAG

Summary for 4UXX

• Entry DOI: 10.2210/pdb4uxx/pdb
• Related: 4UXW 4UXZ
• Descriptor: DIACYLGLYCEROL KINASE, CHLORIDE ION, SODIUM ION, ... (9 entities in total)
• Functional Keywords: 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
• Biological source: ESCHERICHIA COLI K-12
• Total number of polymer chains: 3
• Total formula weight: 45896.58

Authors

Li, D.,Vogeley, L.,Caffrey, M. (deposition date: 2014-08-27, release date: 2015-09-30, Last modification date: 2024-01-10)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.701 Å)