6nyo: Difference between revisions

Latest revision as of 07:01, 11 October 2023

Crystal structure of a human Cdc34-ubiquitin thioester mimetic

Structural highlights

6nyo is a 2 chain structure with sequence from Homo sapiens and Schizosaccharomyces pombe. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.502Å
Ligands:	EDO, PO4, U94
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UB2R2_HUMAN Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes monoubiquitination and 'Lys-48'-linked polyubiquitination. May be involved in degradation of katenin.^[1] ^[2]

Publication Abstract from PubMed

Ubiquitin (Ub) signaling requires the sequential interactions and activities of three enzymes, E1, E2, and E3. Cdc34 is an E2 that plays a key role in regulating cell cycle progression and requires unique structural elements to function. The molecular basis by which Cdc34 engages its E1 and the structural mechanisms by which its unique C-terminal extension functions in Cdc34 activity are unknown. Here, we present crystal structures of Cdc34 alone and in complex with E1, and a Cdc34~Ub thioester mimetic that represents the product of Uba1-Cdc34 Ub transthiolation. These structures reveal conformational changes in Uba1 and Cdc34 and a unique binding mode that are required for transthiolation. The Cdc34~Ub structure reveals contacts between the Cdc34 C-terminal extension and Ub that stabilize Cdc34~Ub in a closed conformation and are critical for Ub discharge. Altogether, our structural, biochemical, and cell-based studies provide insights into the molecular mechanisms by which Cdc34 function in cells.

Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34.,Williams KM, Qie S, Atkison JH, Salazar-Arango S, Alan Diehl J, Olsen SK Nat Commun. 2019 Jul 24;10(1):3296. doi: 10.1038/s41467-019-11061-8. PMID:31341161^[3]

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

References

↑ Semplici F, Meggio F, Pinna LA, Oliviero S. CK2-dependent phosphorylation of the E2 ubiquitin conjugating enzyme UBC3B induces its interaction with beta-TrCP and enhances beta-catenin degradation. Oncogene. 2002 Jun 6;21(25):3978-87. PMID:12037680 doi:10.1038/sj.onc.1205574
↑ David Y, Ziv T, Admon A, Navon A. The E2 ubiquitin conjugating enzymes direct polyubiquitination to preferred lysines. J Biol Chem. 2010 Jan 8. PMID:20061386 doi:M109.089003
↑ Williams KM, Qie S, Atkison JH, Salazar-Arango S, Alan Diehl J, Olsen SK. Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Nat Commun. 2019 Jul 24;10(1):3296. doi: 10.1038/s41467-019-11061-8. PMID:31341161 doi:https://dx.doi.org/10.1038/s41467-019-11061-8

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Semplici F, Meggio F, Pinna LA, Oliviero S. CK2-dependent phosphorylation of the E2 ubiquitin conjugating enzyme UBC3B induces its interaction with beta-TrCP and enhances beta-catenin degradation. Oncogene. 2002 Jun 6;21(25):3978-87. PMID:12037680 doi:10.1038/sj.onc.1205574

[2] David Y, Ziv T, Admon A, Navon A. The E2 ubiquitin conjugating enzymes direct polyubiquitination to preferred lysines. J Biol Chem. 2010 Jan 8. PMID:20061386 doi:M109.089003

[3] Williams KM, Qie S, Atkison JH, Salazar-Arango S, Alan Diehl J, Olsen SK. Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Nat Commun. 2019 Jul 24;10(1):3296. doi: 10.1038/s41467-019-11061-8. PMID:31341161 doi:https://dx.doi.org/10.1038/s41467-019-11061-8

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='6nyo' size='340' side='right'caption='[[6nyo]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6nyo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NYO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6nyo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NYO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=U94:4,5-DIDEOXY-5-(3,5-DICHLOROBIPHENYL-4-YL)-4-[(METHOXYACETYL)AMINO]-L-ARABINONIC+ACID'>U94</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]] 1.502&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6nya|6nya]], [[6nyd|6nyd]]</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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=U94:4,5-DIDEOXY-5-(3,5-DICHLOROBIPHENYL-4-YL)-4-[(METHOXYACETYL)AMINO]-L-ARABINONIC+ACID'>U94</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBE2R2, CDC34B, UBC3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6nyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nyo OCA], [https://pdbe.org/6nyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nyo RCSB], [https://www.ebi.ac.uk/pdbsum/6nyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nyo ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6nyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nyo OCA], [http://pdbe.org/6nyo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nyo RCSB], [http://www.ebi.ac.uk/pdbsum/6nyo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nyo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UB2R2_HUMAN UB2R2_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes monoubiquitination and 'Lys-48'-linked polyubiquitination. May be involved in degradation of katenin.<ref>PMID:12037680</ref> <ref>PMID:20061386</ref>
+[https://www.uniprot.org/uniprot/UB2R2_HUMAN UB2R2_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes monoubiquitination and 'Lys-48'-linked polyubiquitination. May be involved in degradation of katenin.<ref>PMID:12037680</ref> <ref>PMID:20061386</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 19: @@
 </div>
 <div class="pdbe-citations 6nyo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cbs 356]]
+[[Category: Homo sapiens]]
-[[Category: E2 ubiquitin-conjugating enzyme]]
-[[Category: Human]]
 [[Category: Large Structures]]
-[[Category: Atkison, J H]]
+[[Category: Schizosaccharomyces pombe]]
-[[Category: Olsen, S K]]
+[[Category: Atkison JH]]
-[[Category: Williams, K M]]
+[[Category: Olsen SK]]
-[[Category: Adenylation]]
+[[Category: Williams KM]]
-[[Category: Atp-binding]]
-[[Category: Conformational change]]
-[[Category: Ligase]]
-[[Category: Ligase-transferase complex]]
-[[Category: Thioester]]
-[[Category: Thioester transfer]]
-[[Category: Transthioesterification]]
-[[Category: Ubiquitin e2-binding]]
-[[Category: Ubiquitination]]

6nyo: Difference between revisions

Latest revision as of 07:01, 11 October 2023

Crystal structure of a human Cdc34-ubiquitin thioester mimetic

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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