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4uxw

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==Structure of delta4-DgkA-apo in 9.9 MAG==
==Structure of delta4-DgkA-apo in 9.9 MAG==
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<StructureSection load='4uxw' size='340' side='right' caption='[[4uxw]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
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<StructureSection load='4uxw' size='340' side='right'caption='[[4uxw]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4uxw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UXW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4uxw]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UXW FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.15&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4uxx|4uxx]], [[4uxz|4uxz]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diacylglycerol_kinase Diacylglycerol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.107 2.7.1.107] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4uxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxw OCA], [https://pdbe.org/4uxw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uxw RCSB], [https://www.ebi.ac.uk/pdbsum/4uxw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxw ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4uxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxw OCA], [http://pdbe.org/4uxw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uxw RCSB], [http://www.ebi.ac.uk/pdbsum/4uxw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxw ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI]] Recycling of diacylglycerol produced during the turnover of membrane phospholipid.
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[https://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI] Recycling of diacylglycerol produced during the turnover of membrane phospholipid.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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 gamma-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.
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Ternary structure reveals mechanism of a membrane diacylglycerol kinase.,Li D, Stansfeld PJ, Sansom MS, Keogh A, Vogeley L, Howe N, Lyons JA, Aragao D, Fromme P, Fromme R, Basu S, Grotjohann I, Kupitz C, Rendek K, Weierstall U, Zatsepin NA, Cherezov V, Liu W, Bandaru S, English NJ, Gati C, Barty A, Yefanov O, Chapman HN, Diederichs K, Messerschmidt M, Boutet S, Williams GJ, Marvin Seibert M, Caffrey M Nat Commun. 2015 Dec 17;6:10140. doi: 10.1038/ncomms10140. PMID:26673816<ref>PMID:26673816</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4uxw" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Diacylglycerol kinase|Diacylglycerol kinase]]
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*[[Diacylglycerol kinase 3D structures|Diacylglycerol kinase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Diacylglycerol kinase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Ecoli]]
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[[Category: Large Structures]]
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[[Category: Aragao, D]]
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[[Category: Aragao D]]
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[[Category: Caffrey, M]]
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[[Category: Caffrey M]]
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[[Category: Li, D]]
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[[Category: Li D]]
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[[Category: Pye, V E]]
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[[Category: Pye VE]]
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[[Category: Dgka]]
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[[Category: In meso crystallization]]
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[[Category: Lipid cubic phase]]
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[[Category: Lipidic cubic phase]]
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[[Category: Lipidic mesophase]]
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[[Category: Membrane protein]]
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[[Category: Monoacylglycerol]]
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[[Category: Transferase]]
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Current revision

Structure of delta4-DgkA-apo in 9.9 MAG

PDB ID 4uxw

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