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6nya

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Revision as of 11:44, 1 January 2020

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

Structural highlights

6nya is a 6 chain structure with sequence from Baker's yeast and Canadian hard winter wheat. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Gene:	UBA1, YKL210W (Baker's yeast), CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C (Baker's yeast)
Activity:	E1 ubiquitin-activating enzyme, with EC number 6.2.1.45
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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. [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.

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 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 [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Canadian_hard_winter_wheat Canadian hard winter wheat]. 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>
 </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>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBA1, YKL210W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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='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>
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Baker's yeast]]
+[[Category: Canadian hard winter wheat]]
 [[Category: E1 ubiquitin-activating enzyme]]
 [[Category: Large Structures]]

6nya

From Proteopedia

Revision as of 11:44, 1 January 2020

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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