6y5p: Difference between revisions

Latest revision as of 06:27, 1 October 2025

RING-DTC domain of Deltex1 bound to NAD

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.74Å
Ligands:	EDO, NAD, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin's Gly(76) Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD(+) Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD(+) bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.

Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases.,Chatrin C, Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sumpton D, Sibbet GJ, Smith BO, Huang DT Sci Adv. 2020 Sep 18;6(38). pii: 6/38/eabc0418. doi: 10.1126/sciadv.abc0418., Print 2020 Sep. PMID:32948590^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Chatrin C, Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sumpton D, Sibbet GJ, Smith BO, Huang DT. Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases. Sci Adv. 2020 Sep 18;6(38). pii: 6/38/eabc0418. doi: 10.1126/sciadv.abc0418., Print 2020 Sep. PMID:32948590 doi:https://dx.doi.org/10.1126/sciadv.abc0418

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OCA

[1] Chatrin C, Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sumpton D, Sibbet GJ, Smith BO, Huang DT. Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases. Sci Adv. 2020 Sep 18;6(38). pii: 6/38/eabc0418. doi: 10.1126/sciadv.abc0418., Print 2020 Sep. PMID:32948590 doi:https://dx.doi.org/10.1126/sciadv.abc0418

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6y5p' size='340' side='right'caption='[[6y5p]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6y5p]] 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=6Y5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y5P FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y5P 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]] 1.74&#8491;</td></tr>
 <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6y5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y5p OCA], [https://pdbe.org/6y5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y5p RCSB], [https://www.ebi.ac.uk/pdbsum/6y5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y5p ProSAT]</span></td></tr>
 </table>
-== Function ==
-[https://www.uniprot.org/uniprot/DTX1_HUMAN DTX1_HUMAN] Functions as a ubiquitin ligase protein in vivo, mediating ubiquitination and promoting degradation of MEKK1, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity (By similarity). Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Mainly acts as a positive regulator of Notch, but it also acts as a negative regulator, depending on the developmental and cell context. Mediates the antineural activity of Notch, possibly by inhibiting the transcriptional activation mediated by MATCH1. Involved in neurogenesis, lymphogenesis and myogenesis, and may also be involved in MZB (Marginal zone B) cell differentiation. Promotes B-cell development at the expense of T-cell development, suggesting that it can antagonize NOTCH1.<ref>PMID:11564735</ref> <ref>PMID:11869684</ref> <ref>PMID:9590294</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 24: @@
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
 [[Category: Large Structures]]
 [[Category: Buetow L]]
 [[Category: Gabrielsen M]]
 [[Category: Huang DT]]

6y5p: Difference between revisions

Latest revision as of 06:27, 1 October 2025

RING-DTC domain of Deltex1 bound to NAD

Structural highlights

Publication Abstract from PubMed

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References

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