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| | ==Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18 angstrom resolution== | | ==Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18 angstrom resolution== |
| - | <StructureSection load='4uyo' size='340' side='right' caption='[[4uyo]], [[Resolution|resolution]] 2.18Å' scene=''> | + | <StructureSection load='4uyo' size='340' side='right'caption='[[4uyo]], [[Resolution|resolution]] 2.18Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4uyo]] is a 6 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=4UYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UYO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4uyo]] is a 6 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=4UYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UYO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=79M:(2R)-2,3-DIHYDROXYPROPYL+(7Z)-HEXADEC-7-ENOATE'>79M</scene>, <scene name='pdbligand=79N:(2S)-2,3-DIHYDROXYPROPYL+(7Z)-HEXADEC-7-ENOATE'>79N</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.18Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4uxw|4uxw]], [[4uxx|4uxx]], [[4uxz|4uxz]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=79M:(2R)-2,3-DIHYDROXYPROPYL+(7Z)-HEXADEC-7-ENOATE'>79M</scene>, <scene name='pdbligand=79N:(2S)-2,3-DIHYDROXYPROPYL+(7Z)-HEXADEC-7-ENOATE'>79N</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <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>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4uyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uyo OCA], [https://pdbe.org/4uyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uyo RCSB], [https://www.ebi.ac.uk/pdbsum/4uyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uyo ProSAT]</span></td></tr> |
| - | <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=4uyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uyo OCA], [http://pdbe.org/4uyo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uyo RCSB], [http://www.ebi.ac.uk/pdbsum/4uyo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uyo ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI]] Recycling of diacylglycerol produced during the turnover of membrane phospholipid. | + | [https://www.uniprot.org/uniprot/KDGL_ECOLI KDGL_ECOLI] Recycling of diacylglycerol produced during the turnover of membrane phospholipid. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Diacylglycerol kinase|Diacylglycerol kinase]] | + | *[[Diacylglycerol kinase 3D structures|Diacylglycerol kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Diacylglycerol kinase]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ecoli]] | + | [[Category: Large Structures]] |
| - | [[Category: Caffrey, M]] | + | [[Category: Caffrey M]] |
| - | [[Category: Howe, N]] | + | [[Category: Howe N]] |
| - | [[Category: Li, D]] | + | [[Category: Li D]] |
| - | [[Category: Other, O]] | + | [[Category: Other O]] |
| - | [[Category: 9 mag]]
| + | |
| - | [[Category: In meso crystallization]]
| + | |
| - | [[Category: Lipid cubic phase]]
| + | |
| - | [[Category: Lipid mesophase]]
| + | |
| - | [[Category: Lipidic cubic phase]]
| + | |
| - | [[Category: Lipidic mesophase]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Microcrystal]]
| + | |
| - | [[Category: Monoacylglycerol]]
| + | |
| - | [[Category: Room temperature crystallography]]
| + | |
| - | [[Category: Serial femtosecond crystallography]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: X-ray free-electron laser]]
| + | |
| Structural highlights
Function
KDGL_ECOLI Recycling of diacylglycerol produced during the turnover of membrane phospholipid.
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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. Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Nat Commun. 2015 Dec 17;6:10140. doi: 10.1038/ncomms10140. PMID:26673816 doi:http://dx.doi.org/10.1038/ncomms10140
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