9r0e: Difference between revisions

Latest revision as of 07:27, 29 October 2025

Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249T in complex with magnesium, FsPP and IPP

Structural highlights

9r0e is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.82Å
Ligands:	FPS, IPE, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

DHDDS_HUMAN Retinitis pigmentosa;Non-specific early-onset epileptic encephalopathy. The disease is caused by variants affecting the gene represented in this entry. The disease may be caused by variants affecting the gene represented in this entry.

Function

DHDDS_HUMAN With NUS1, forms the dehydrodolichyl diphosphate synthase (DDS) complex, an essential component of the dolichol monophosphate (Dol-P) biosynthetic machinery (PubMed:25066056, PubMed:28842490, PubMed:32817466, PubMed:33077723). Both subunits contribute to enzymatic activity, i.e. condensation of multiple copies of isopentenyl pyrophosphate (IPP) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (Dedol-PP), a precursor of dolichol phosphate which is utilized as a sugar carrier in protein glycosylation in the endoplasmic reticulum (ER) (PubMed:25066056, PubMed:28842490, PubMed:32817466, PubMed:33077723). Synthesizes long-chain polyprenols, mostly of C95 and C100 chain length (PubMed:32817466). Regulates the glycosylation and stability of nascent NPC2, thereby promoting trafficking of LDL-derived cholesterol (PubMed:21572394).^[1] ^[2] ^[3] ^[4] ^[5]

References

↑ Harrison KD, Park EJ, Gao N, Kuo A, Rush JS, Waechter CJ, Lehrman MA, Sessa WC. Nogo-B receptor is necessary for cellular dolichol biosynthesis and protein N-glycosylation. EMBO J. 2011 May 13;30(12):2490-500. PMID:21572394 doi:10.1038/emboj.2011.147
↑ Park EJ, Grabinska KA, Guan Z, Stranecky V, Hartmannova H, Hodanova K, Baresova V, Sovova J, Jozsef L, Ondruskova N, Hansikova H, Honzik T, Zeman J, Hulkova H, Wen R, Kmoch S, Sessa WC. Mutation of Nogo-B receptor, a subunit of cis-prenyltransferase, causes a congenital disorder of glycosylation. Cell Metab. 2014 Sep 2;20(3):448-57. doi: 10.1016/j.cmet.2014.06.016. Epub 2014, Jul 24. PMID:25066056 doi:https://dx.doi.org/10.1016/j.cmet.2014.06.016
↑ Grabińska KA, Edani BH, Park EJ, Kraehling JR, Sessa WC. A conserved C-terminal RXG motif in the NgBR subunit of cis-prenyltransferase is critical for prenyltransferase activity. J Biol Chem. 2017 Oct 20;292(42):17351-17361. PMID:28842490 doi:10.1074/jbc.M117.806034
↑ Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A. 2020 Aug 25;117(34):20794-20802. PMID:32817466 doi:10.1073/pnas.2008381117
↑ Bar-El ML, Vaňková P, Yeheskel A, Simhaev L, Engel H, Man P, Haitin Y, Giladi M. Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex. Nat Commun. 2020 Oct 19;11(1):5273. PMID:33077723 doi:10.1038/s41467-020-18970-z

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Harrison KD, Park EJ, Gao N, Kuo A, Rush JS, Waechter CJ, Lehrman MA, Sessa WC. Nogo-B receptor is necessary for cellular dolichol biosynthesis and protein N-glycosylation. EMBO J. 2011 May 13;30(12):2490-500. PMID:21572394 doi:10.1038/emboj.2011.147

[2] Park EJ, Grabinska KA, Guan Z, Stranecky V, Hartmannova H, Hodanova K, Baresova V, Sovova J, Jozsef L, Ondruskova N, Hansikova H, Honzik T, Zeman J, Hulkova H, Wen R, Kmoch S, Sessa WC. Mutation of Nogo-B receptor, a subunit of cis-prenyltransferase, causes a congenital disorder of glycosylation. Cell Metab. 2014 Sep 2;20(3):448-57. doi: 10.1016/j.cmet.2014.06.016. Epub 2014, Jul 24. PMID:25066056 doi:https://dx.doi.org/10.1016/j.cmet.2014.06.016

[3] Grabińska KA, Edani BH, Park EJ, Kraehling JR, Sessa WC. A conserved C-terminal RXG motif in the NgBR subunit of cis-prenyltransferase is critical for prenyltransferase activity. J Biol Chem. 2017 Oct 20;292(42):17351-17361. PMID:28842490 doi:10.1074/jbc.M117.806034

[4] Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A. 2020 Aug 25;117(34):20794-20802. PMID:32817466 doi:10.1073/pnas.2008381117

[5] Bar-El ML, Vaňková P, Yeheskel A, Simhaev L, Engel H, Man P, Haitin Y, Giladi M. Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex. Nat Commun. 2020 Oct 19;11(1):5273. PMID:33077723 doi:10.1038/s41467-020-18970-z

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9r0e is ON HOLD  until Paper Publication
+==Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249T in complex with magnesium, FsPP and IPP==
+<StructureSection load='9r0e' size='340' side='right'caption='[[9r0e]], [[Resolution|resolution]] 2.82&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9r0e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9R0E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9R0E FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.82&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FPS:S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL]+TRIHYDROGEN+THIODIPHOSPHATE'>FPS</scene>, <scene name='pdbligand=IPE:3-METHYLBUT-3-ENYL+TRIHYDROGEN+DIPHOSPHATE'>IPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=9r0e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9r0e OCA], [https://pdbe.org/9r0e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9r0e RCSB], [https://www.ebi.ac.uk/pdbsum/9r0e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9r0e ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/DHDDS_HUMAN DHDDS_HUMAN] Retinitis pigmentosa;Non-specific early-onset epileptic encephalopathy. The disease is caused by variants affecting the gene represented in this entry.  The disease may be caused by variants affecting the gene represented in this entry.
+== Function ==
+[https://www.uniprot.org/uniprot/DHDDS_HUMAN DHDDS_HUMAN] With NUS1, forms the dehydrodolichyl diphosphate synthase (DDS) complex, an essential component of the dolichol monophosphate (Dol-P) biosynthetic machinery (PubMed:25066056, PubMed:28842490, PubMed:32817466, PubMed:33077723). Both subunits contribute to enzymatic activity, i.e. condensation of multiple copies of isopentenyl pyrophosphate (IPP) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (Dedol-PP), a precursor of dolichol phosphate which is utilized as a sugar carrier in protein glycosylation in the endoplasmic reticulum (ER) (PubMed:25066056, PubMed:28842490, PubMed:32817466, PubMed:33077723). Synthesizes long-chain polyprenols, mostly of C95 and C100 chain length (PubMed:32817466). Regulates the glycosylation and stability of nascent NPC2, thereby promoting trafficking of LDL-derived cholesterol (PubMed:21572394).<ref>PMID:21572394</ref> <ref>PMID:25066056</ref> <ref>PMID:28842490</ref> <ref>PMID:32817466</ref> <ref>PMID:33077723</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Giladi M]]
+[[Category: Haitin Y]]

9r0e: Difference between revisions

Latest revision as of 07:27, 29 October 2025

Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249T in complex with magnesium, FsPP and IPP

Structural highlights

Disease

Function

References

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