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| | <StructureSection load='7pp7' size='340' side='right'caption='[[7pp7]], [[Resolution|resolution]] 2.05Å' scene=''> | | <StructureSection load='7pp7' size='340' side='right'caption='[[7pp7]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7pp7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PP7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7pp7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thunbergia_alata Thunbergia alata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PP7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 2.05Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acyl-[acyl-carrier-protein]_6-desaturase Acyl-[acyl-carrier-protein] 6-desaturase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.19.26 1.14.19.26] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></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=7pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pp7 OCA], [https://pdbe.org/7pp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pp7 RCSB], [https://www.ebi.ac.uk/pdbsum/7pp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pp7 ProSAT]</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=7pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pp7 OCA], [https://pdbe.org/7pp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pp7 RCSB], [https://www.ebi.ac.uk/pdbsum/7pp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pp7 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/PALAD_THUAT PALAD_THUAT]] Delta(6) fatty acid desaturase introducing a cis double bond at carbon 6 of palmitoyl-[acyl-carrier protein](16:0-ACP), producing 16:1(6Z)-ACP (PubMed:7961667, PubMed:9144157). No activity with the coenzyme A ester of the fatty acid (PubMed:7961667). The position of the double bond is determined by its distance from the carboxyl end of the fatty acid (PubMed:7961667). Low activity with several saturated acyl-[acyl-carrier protein]s, including 14:0-ACP and 18:0-ACP (PubMed:7961667, PubMed:9144157). Requires reduced ferredoxin for detectable in vitro activity (PubMed:7961667).<ref>PMID:7961667</ref> <ref>PMID:9144157</ref>
| + | [https://www.uniprot.org/uniprot/PALAD_THUAT PALAD_THUAT] Delta(6) fatty acid desaturase introducing a cis double bond at carbon 6 of palmitoyl-[acyl-carrier protein](16:0-ACP), producing 16:1(6Z)-ACP (PubMed:7961667, PubMed:9144157). No activity with the coenzyme A ester of the fatty acid (PubMed:7961667). The position of the double bond is determined by its distance from the carboxyl end of the fatty acid (PubMed:7961667). Low activity with several saturated acyl-[acyl-carrier protein]s, including 14:0-ACP and 18:0-ACP (PubMed:7961667, PubMed:9144157). Requires reduced ferredoxin for detectable in vitro activity (PubMed:7961667).<ref>PMID:7961667</ref> <ref>PMID:9144157</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cai, Y]] | + | [[Category: Thunbergia alata]] |
| - | [[Category: Chai, J]] | + | [[Category: Cai Y]] |
| - | [[Category: Guy, J E]] | + | [[Category: Chai J]] |
| - | [[Category: Lindqvist, Y]] | + | [[Category: Guy JE]] |
| - | [[Category: Shanklin, J]] | + | [[Category: Lindqvist Y]] |
| - | [[Category: Whittle, E]] | + | [[Category: Shanklin J]] |
| - | [[Category: Desaturase]]
| + | [[Category: Whittle E]] |
| - | [[Category: Di-iron protein]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
PALAD_THUAT Delta(6) fatty acid desaturase introducing a cis double bond at carbon 6 of palmitoyl-[acyl-carrier protein](16:0-ACP), producing 16:1(6Z)-ACP (PubMed:7961667, PubMed:9144157). No activity with the coenzyme A ester of the fatty acid (PubMed:7961667). The position of the double bond is determined by its distance from the carboxyl end of the fatty acid (PubMed:7961667). Low activity with several saturated acyl-[acyl-carrier protein]s, including 14:0-ACP and 18:0-ACP (PubMed:7961667, PubMed:9144157). Requires reduced ferredoxin for detectable in vitro activity (PubMed:7961667).[1] [2]
Publication Abstract from PubMed
Plant plastidial acyl-acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Delta9cis)-ACP. Several variants expressing distinct regioselectivity have been described including a Delta6-16:0-ACP desaturase from black-eyed Susan vine (Thunbergia alata). We solved a crystal structure of the T. alata desaturase at 2.05 A resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Delta6 desaturase to Delta9 regioselectivity. Additional modelling between ACP and the mutant variants confirmed the predicted regioselectivity. To validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Delta6 to Delta9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Delta9 to Delta6 selectivity lost some of their Delta9 desaturation ability and gained the ability to desaturate at the Delta6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.
Regioselectivity mechanism of the Thunbergia alata Delta6-16:0-acyl carrier protein desaturase.,Guy JE, Cai Y, Baer MD, Whittle E, Chai J, Yu XH, Lindqvist Y, Raugei S, Shanklin J Plant Physiol. 2021 Dec 10. pii: 6459183. doi: 10.1093/plphys/kiab577. PMID:34893899[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Cahoon EB, Cranmer AM, Shanklin J, Ohlrogge JB. delta 6 Hexadecenoic acid is synthesized by the activity of a soluble delta 6 palmitoyl-acyl carrier protein desaturase in Thunbergia alata endosperm. J Biol Chem. 1994 Nov 4;269(44):27519-26. PMID:7961667
- ↑ Cahoon EB, Lindqvist Y, Schneider G, Shanklin J. Redesign of soluble fatty acid desaturases from plants for altered substrate specificity and double bond position. Proc Natl Acad Sci U S A. 1997 May 13;94(10):4872-7. doi:, 10.1073/pnas.94.10.4872. PMID:9144157 doi:http://dx.doi.org/10.1073/pnas.94.10.4872
- ↑ Guy JE, Cai Y, Baer MD, Whittle E, Chai J, Yu XH, Lindqvist Y, Raugei S, Shanklin J. Regioselectivity mechanism of the Thunbergia alata Delta6-16:0-acyl carrier protein desaturase. Plant Physiol. 2021 Dec 10. pii: 6459183. doi: 10.1093/plphys/kiab577. PMID:34893899 doi:http://dx.doi.org/10.1093/plphys/kiab577
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