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6nya

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Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin

Structural highlights

6nya is a 6 chain structure with sequence from Saccharomyces cerevisiae S288C and Triticum aestivum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.065Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBIQ_WHEAT Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).

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^[1]

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

References

↑ 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:http://dx.doi.org/10.1038/s41467-019-11061-8

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6nya"

@@ Line 3: / Line 3: @@
 <StructureSection load='6nya' size='340' side='right'caption='[[6nya]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6nya]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NYA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NYA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6nya]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Triticum_aestivum Triticum aestivum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NYA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.065&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E1_ubiquitin-activating_enzyme E1 ubiquitin-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.45 6.2.1.45] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6nya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nya OCA], [http://pdbe.org/6nya PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nya RCSB], [http://www.ebi.ac.uk/pdbsum/6nya PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nya 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=6nya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nya OCA], [https://pdbe.org/6nya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nya RCSB], [https://www.ebi.ac.uk/pdbsum/6nya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nya ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UBA1_YEAST UBA1_YEAST]] Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thioester and free AMP. [[http://www.uniprot.org/uniprot/UBC3_YEAST UBC3_YEAST]] Catalyzes the covalent attachment of ubiquitin to other proteins. Capable, in vitro, to ubiquitinate histone H2A.  Mediates the initiation of DNA replication (transition of G1 to S phase in cell cycle). Essential component of the E3 ubiquitin ligase complex SCF (SKP1-CUL1-F-box protein), which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Involved in the regulation of methionine biosynthesis genes and in the degradation of CDC6 together with CDC4 and CDC53.
+[https://www.uniprot.org/uniprot/UBIQ_WHEAT UBIQ_WHEAT] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6nya" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[3D structures of Ubiquitin activating enzyme|3D structures of Ubiquitin activating enzyme]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: E1 ubiquitin-activating enzyme]]
 [[Category: Large Structures]]
-[[Category: Atkison, J H]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Olsen, S K]]
+[[Category: Triticum aestivum]]
-[[Category: Williams, K M]]
+[[Category: Atkison JH]]
-[[Category: Adenylation]]
+[[Category: Olsen SK]]
-[[Category: Atp-binding]]
+[[Category: Williams KM]]
-[[Category: Conformational change]]
-[[Category: Ligase]]
-[[Category: Ligase-transferase complex]]
-[[Category: Thioester]]
-[[Category: Thioester transfer]]
-[[Category: Transthioesterification]]
-[[Category: Ubiquitin e2-binding]]
-[[Category: Ubiquitination]]

6nya

From Proteopedia

Current revision

Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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