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| | <StructureSection load='6l07' size='340' side='right'caption='[[6l07]], [[Resolution|resolution]] 3.60Å' scene=''> | | <StructureSection load='6l07' size='340' side='right'caption='[[6l07]], [[Resolution|resolution]] 3.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6l07]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L07 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L07 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6l07]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L07 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L07 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</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]] 3.6Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphatidylserine_decarboxylase Phosphatidylserine decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.65 4.1.1.65] </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=6l07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l07 OCA], [https://pdbe.org/6l07 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l07 RCSB], [https://www.ebi.ac.uk/pdbsum/6l07 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l07 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=6l07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l07 OCA], [https://pdbe.org/6l07 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l07 RCSB], [https://www.ebi.ac.uk/pdbsum/6l07 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l07 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/A0A446DLT6_ECOLX A0A446DLT6_ECOLX]] Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer).[HAMAP-Rule:MF_00662][SAAS:SAAS00970414]
| + | [https://www.uniprot.org/uniprot/PSD_ECOLI PSD_ECOLI] Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Only decarboxylates the lipid-linked form of the serine moiety, and not serine alone or derivatives like phosphoserine or glycerophosphoserine.[HAMAP-Rule:MF_00662]<ref>PMID:4598120</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecobd]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Phosphatidylserine decarboxylase]]
| + | [[Category: Watanabe S]] |
| - | [[Category: Watanabe, S]] | + | [[Category: Watanabe Y]] |
| - | [[Category: Watanabe, Y]] | + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Phosphatidylethanolamine]]
| + | |
| - | [[Category: Phosphatidylserine]]
| + | |
| Structural highlights
Function
PSD_ECOLI Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Only decarboxylates the lipid-linked form of the serine moiety, and not serine alone or derivatives like phosphoserine or glycerophosphoserine.[HAMAP-Rule:MF_00662][1]
Publication Abstract from PubMed
In both prokaryotes and eukaryotes, phosphatidylethanolamine (PE), one of the most abundant membrane phospholipids, plays important roles in various membrane functions and is synthesized through the decarboxylation of phosphatidylserine (PS) by PS decarboxylases (PSDs). However, the catalysis and substrate recognition mechanisms of PSDs remain unclear. In this study, we focused on the PSD from Escherichia coli (EcPsd) and determined the crystal structures of EcPsd in the apo form and PE-bound form at resolutions of 2.6 and 3.6 A, respectively. EcPsd forms a homodimer, and each protomer has a positively charged substrate binding pocket at the active site. Structure-based mutational analyses revealed that conserved residues in the pocket are involved in PS decarboxylation. EcPsd has an N-terminal hydrophobic helical region that is important for membrane binding, thereby achieving efficient PS recognition. These results provide a structural basis for understanding the mechanism of PE biosynthesis by PSDs.
Structural Basis for Phosphatidylethanolamine Biosynthesis by Bacterial Phosphatidylserine Decarboxylase.,Watanabe Y, Watanabe Y, Watanabe S Structure. 2020 Apr 24. pii: S0969-2126(20)30125-8. doi:, 10.1016/j.str.2020.04.006. PMID:32402247[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dowhan W, Wickner WT, Kennedy EP. Purification and properties of phosphatidylserine decarboxylase from Escherichia coli. J Biol Chem. 1974 May 25;249(10):3079-84 PMID:4598120
- ↑ Watanabe Y, Watanabe Y, Watanabe S. Structural Basis for Phosphatidylethanolamine Biosynthesis by Bacterial Phosphatidylserine Decarboxylase. Structure. 2020 Apr 24. pii: S0969-2126(20)30125-8. doi:, 10.1016/j.str.2020.04.006. PMID:32402247 doi:http://dx.doi.org/10.1016/j.str.2020.04.006
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