8iak: Difference between revisions

Latest revision as of 11:30, 18 June 2025

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A-N71A) complex

Structural highlights

8iak is a 8 chain structure with sequence from Arabidopsis thaliana, Saccharomyces cerevisiae and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.1Å
Ligands:	LLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPTC1_YEAST Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine.^[1] ^[2] SPTC1_ARATH Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine. The heterodimer formed with LCB2 constitutes the catalytic core. Involved in the regulation of the programmed cell death (PCD) signaling pathway. Plays an important role during male gametogenesis and embryogenesis.^[3] ^[4] ^[5]

References

↑ Gable K, Han G, Monaghan E, Bacikova D, Natarajan M, Williams R, Dunn TM. Mutations in the yeast LCB1 and LCB2 genes, including those corresponding to the hereditary sensory neuropathy type I mutations, dominantly inactivate serine palmitoyltransferase. J Biol Chem. 2002 Mar 22;277(12):10194-200. PMID:11781309 doi:10.1074/jbc.M107873200
↑ Nagiec MM, Baltisberger JA, Wells GB, Lester RL, Dickson RC. The LCB2 gene of Saccharomyces and the related LCB1 gene encode subunits of serine palmitoyltransferase, the initial enzyme in sphingolipid synthesis. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):7899-902. PMID:8058731 doi:10.1073/pnas.91.17.7899
↑ Chen M, Han G, Dietrich CR, Dunn TM, Cahoon EB. The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase. Plant Cell. 2006 Dec;18(12):3576-93. PMID:17194770 doi:10.1105/tpc.105.040774
↑ Shi L, Bielawski J, Mu J, Dong H, Teng C, Zhang J, Yang X, Tomishige N, Hanada K, Hannun YA, Zuo J. Involvement of sphingoid bases in mediating reactive oxygen intermediate production and programmed cell death in Arabidopsis. Cell Res. 2007 Dec;17(12):1030-40. PMID:18059378 doi:10.1038/cr.2007.100
↑ Teng C, Dong H, Shi L, Deng Y, Mu J, Zhang J, Yang X, Zuo J. Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis. Plant Physiol. 2008 Mar;146(3):1322-32. PMID:18218968 doi:10.1104/pp.107.113506

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OCA

[1] Gable K, Han G, Monaghan E, Bacikova D, Natarajan M, Williams R, Dunn TM. Mutations in the yeast LCB1 and LCB2 genes, including those corresponding to the hereditary sensory neuropathy type I mutations, dominantly inactivate serine palmitoyltransferase. J Biol Chem. 2002 Mar 22;277(12):10194-200. PMID:11781309 doi:10.1074/jbc.M107873200

[2] Nagiec MM, Baltisberger JA, Wells GB, Lester RL, Dickson RC. The LCB2 gene of Saccharomyces and the related LCB1 gene encode subunits of serine palmitoyltransferase, the initial enzyme in sphingolipid synthesis. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):7899-902. PMID:8058731 doi:10.1073/pnas.91.17.7899

[3] Chen M, Han G, Dietrich CR, Dunn TM, Cahoon EB. The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase. Plant Cell. 2006 Dec;18(12):3576-93. PMID:17194770 doi:10.1105/tpc.105.040774

[4] Shi L, Bielawski J, Mu J, Dong H, Teng C, Zhang J, Yang X, Tomishige N, Hanada K, Hannun YA, Zuo J. Involvement of sphingoid bases in mediating reactive oxygen intermediate production and programmed cell death in Arabidopsis. Cell Res. 2007 Dec;17(12):1030-40. PMID:18059378 doi:10.1038/cr.2007.100

[5] Teng C, Dong H, Shi L, Deng Y, Mu J, Zhang J, Yang X, Zuo J. Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis. Plant Physiol. 2008 Mar;146(3):1322-32. PMID:18218968 doi:10.1104/pp.107.113506

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@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[8iak]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana], [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IAK FirstGlance]. <br>
 </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=8iak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8iak OCA], [https://pdbe.org/8iak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8iak RCSB], [https://www.ebi.ac.uk/pdbsum/8iak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8iak ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/LCB1_YEAST LCB1_YEAST] Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine.<ref>PMID:11781309</ref> <ref>PMID:8058731</ref> [https://www.uniprot.org/uniprot/LCB1_ARATH LCB1_ARATH] Serine palmitoyltransferase (SPT). The heterodimer formed with LCB2 constitutes the catalytic core. Involved in the regulation of the programmed cell death (PCD) signaling pathway. Plays an important role during male gametogenesis and embryogenesis.<ref>PMID:17194770</ref> <ref>PMID:18059378</ref> <ref>PMID:18218968</ref>
+[https://www.uniprot.org/uniprot/SPTC1_YEAST SPTC1_YEAST] Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine.<ref>PMID:11781309</ref> <ref>PMID:8058731</ref> [https://www.uniprot.org/uniprot/SPTC1_ARATH SPTC1_ARATH] Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine. The heterodimer formed with LCB2 constitutes the catalytic core. Involved in the regulation of the programmed cell death (PCD) signaling pathway. Plays an important role during male gametogenesis and embryogenesis.<ref>PMID:17194770</ref> <ref>PMID:18059378</ref> <ref>PMID:18218968</ref>
 == References ==
 <references/>

8iak: Difference between revisions

Latest revision as of 11:30, 18 June 2025

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A-N71A) complex

Structural highlights

Function

References

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