6zqh: Difference between revisions
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==== | ==Yeast Uba1 in complex with ubiquitin== | ||
<StructureSection load='6zqh' size='340' side='right'caption='[[6zqh]]' scene=''> | <StructureSection load='6zqh' size='340' side='right'caption='[[6zqh]], [[Resolution|resolution]] 2.03Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[6zqh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZQH FirstGlance]. <br> | ||
</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=6zqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zqh OCA], [https://pdbe.org/6zqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zqh RCSB], [https://www.ebi.ac.uk/pdbsum/6zqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zqh ProSAT]</span></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]] 2.032Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=6zqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zqh OCA], [https://pdbe.org/6zqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zqh RCSB], [https://www.ebi.ac.uk/pdbsum/6zqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zqh ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://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. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Legionnaires' disease is caused by infection with the intracellularly replicating Gram-negative bacterium Legionella pneumophila. This pathogen uses an unconventional way of ubiquitinating host proteins by generating a phosphoribosyl linkage between substrate proteins and ubiquitin by making use of an ADPribosylated ubiquitin (Ub(ADPr) ) intermediate. The family of SidE effector enzymes that catalyze this reaction is counteracted by Legionella hydrolases, which are called Dups. This unusual ubiquitination process is important for Legionella proliferation and understanding these processes on a molecular level might prove invaluable in finding new treatments. Herein, a modular approach is used for the synthesis of triazole-linked Ub(ADPr) , and analogues thereof, and their affinity towards the hydrolase DupA is determined and hydrolysis rates are compared to natively linked Ub(ADPr) . The inhibitory effects of modified Ub on the canonical eukaryotic E1-enzyme Uba1 are investigated and rationalized in the context of a high-resolution crystal structure reported herein. Finally, it is shown that synthetic Ub(ADPr) analogues can be used to effectively pull-down overexpressed DupA from cell lysate. | |||
Development of ADPribosyl Ubiquitin Analogues to Study Enzymes Involved in Legionella Infection.,Kim RQ, Misra M, Gonzalez A, Tomaskovic I, Shin D, Schindelin H, Filippov DV, Ovaa H, Dikic I, van der Heden van Noort GJ Chemistry. 2021 Feb 1;27(7):2506-2512. doi: 10.1002/chem.202004590. Epub 2020 Dec , 23. PMID:33075184<ref>PMID:33075184</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6zqh" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[3D structures of Ubiquitin activating enzyme|3D structures of Ubiquitin activating enzyme]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Misra M]] | |||
[[Category: Schindelin H]] | |||
Latest revision as of 14:56, 1 February 2024
Yeast Uba1 in complex with ubiquitinYeast Uba1 in complex with ubiquitin
Structural highlights
FunctionUBA1_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. Publication Abstract from PubMedLegionnaires' disease is caused by infection with the intracellularly replicating Gram-negative bacterium Legionella pneumophila. This pathogen uses an unconventional way of ubiquitinating host proteins by generating a phosphoribosyl linkage between substrate proteins and ubiquitin by making use of an ADPribosylated ubiquitin (Ub(ADPr) ) intermediate. The family of SidE effector enzymes that catalyze this reaction is counteracted by Legionella hydrolases, which are called Dups. This unusual ubiquitination process is important for Legionella proliferation and understanding these processes on a molecular level might prove invaluable in finding new treatments. Herein, a modular approach is used for the synthesis of triazole-linked Ub(ADPr) , and analogues thereof, and their affinity towards the hydrolase DupA is determined and hydrolysis rates are compared to natively linked Ub(ADPr) . The inhibitory effects of modified Ub on the canonical eukaryotic E1-enzyme Uba1 are investigated and rationalized in the context of a high-resolution crystal structure reported herein. Finally, it is shown that synthetic Ub(ADPr) analogues can be used to effectively pull-down overexpressed DupA from cell lysate. Development of ADPribosyl Ubiquitin Analogues to Study Enzymes Involved in Legionella Infection.,Kim RQ, Misra M, Gonzalez A, Tomaskovic I, Shin D, Schindelin H, Filippov DV, Ovaa H, Dikic I, van der Heden van Noort GJ Chemistry. 2021 Feb 1;27(7):2506-2512. doi: 10.1002/chem.202004590. Epub 2020 Dec , 23. PMID:33075184[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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