6lkc: Difference between revisions
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The | ==Crystal structure of PfaD from Shewanella piezotolerans in complex with FMN== | ||
<StructureSection load='6lkc' size='340' side='right'caption='[[6lkc]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6lkc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_piezotolerans_WP3 Shewanella piezotolerans WP3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LKC FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.998Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6lkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lkc OCA], [https://pdbe.org/6lkc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lkc RCSB], [https://www.ebi.ac.uk/pdbsum/6lkc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lkc ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/B8CQB6_SHEPW B8CQB6_SHEPW] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Two long-chain polyunsaturated fatty acids (LC-PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), play vital roles in human health. Similarly, two biosynthetic pathways, based on desaturase/elongase and polyketide synthase, have been implicated in the synthesis of microbial LC-PUFA. Up to now, only several microalgae, no bacteria, have been used in the commercial production of oils rich in DHA and/or EPA. Fully understanding the enzymatic mechanism in the biosynthesis of LC-PUFA would contribute significantly to produce EPA and/or DHA by the bacteria. In this study, we report a 1.998 A-resolution crystal structure of trans-acting enoyl reductase (ER), SpPfaD, from Shewanella piezotolerans. The SpPfaD model consists of one homodimer in the asymmetric unit, and each subunit contains three domains. These include an N-terminal, a central domain forming a classic TIM barrel with a single FMN cofactor molecule bound atop the barrel, and a C-terminal domain with a lid above the TIM barrel. Furthermore, we docked oxidized nicotinamide adenine dinucleotide phosphate (NADP) and an inhibitor 2-(4-(2-((3-(5-(pyridin-2-ylthio)thiazol-2-yl)ureido)methyl)-1H-imidazole-4-yl)ph enoxy)acetic acid (TUI) molecule into the active site and analyzed the inhibition and catalytic mechanisms of the enoyl reductase SpPfaD. To the best of our knowledge, this is the first crystal structure of trans-ER in the biosynthesis of bacterial polyketides. | |||
Structural Insights into the Trans-Acting Enoyl Reductase in the Biosynthesis of Long-Chain Polyunsaturated Fatty Acids in Shewanella piezotolerans.,Zhang M, Zhang H, Li Q, Gao Y, Guo L, He L, Zang S, Guo X, Huang J, Li L J Agric Food Chem. 2021 Feb 24;69(7):2316-2324. doi: 10.1021/acs.jafc.0c07386., Epub 2021 Feb 15. PMID:33587627<ref>PMID:33587627</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Guo | <div class="pdbe-citations 6lkc" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: Li | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Shewanella piezotolerans WP3]] | ||
[[Category: Zhang | [[Category: Guo LJ]] | ||
[[Category: He L]] | |||
[[Category: Huang JZ]] | |||
[[Category: Li L]] | |||
[[Category: Li Q]] | |||
[[Category: Meng SS]] | |||
[[Category: Zhang HD]] | |||
[[Category: Zhang ML]] | |||
Latest revision as of 14:02, 22 November 2023
Crystal structure of PfaD from Shewanella piezotolerans in complex with FMNCrystal structure of PfaD from Shewanella piezotolerans in complex with FMN
Structural highlights
FunctionPublication Abstract from PubMedTwo long-chain polyunsaturated fatty acids (LC-PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), play vital roles in human health. Similarly, two biosynthetic pathways, based on desaturase/elongase and polyketide synthase, have been implicated in the synthesis of microbial LC-PUFA. Up to now, only several microalgae, no bacteria, have been used in the commercial production of oils rich in DHA and/or EPA. Fully understanding the enzymatic mechanism in the biosynthesis of LC-PUFA would contribute significantly to produce EPA and/or DHA by the bacteria. In this study, we report a 1.998 A-resolution crystal structure of trans-acting enoyl reductase (ER), SpPfaD, from Shewanella piezotolerans. The SpPfaD model consists of one homodimer in the asymmetric unit, and each subunit contains three domains. These include an N-terminal, a central domain forming a classic TIM barrel with a single FMN cofactor molecule bound atop the barrel, and a C-terminal domain with a lid above the TIM barrel. Furthermore, we docked oxidized nicotinamide adenine dinucleotide phosphate (NADP) and an inhibitor 2-(4-(2-((3-(5-(pyridin-2-ylthio)thiazol-2-yl)ureido)methyl)-1H-imidazole-4-yl)ph enoxy)acetic acid (TUI) molecule into the active site and analyzed the inhibition and catalytic mechanisms of the enoyl reductase SpPfaD. To the best of our knowledge, this is the first crystal structure of trans-ER in the biosynthesis of bacterial polyketides. Structural Insights into the Trans-Acting Enoyl Reductase in the Biosynthesis of Long-Chain Polyunsaturated Fatty Acids in Shewanella piezotolerans.,Zhang M, Zhang H, Li Q, Gao Y, Guo L, He L, Zang S, Guo X, Huang J, Li L J Agric Food Chem. 2021 Feb 24;69(7):2316-2324. doi: 10.1021/acs.jafc.0c07386., Epub 2021 Feb 15. PMID:33587627[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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