5yec: Difference between revisions

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<StructureSection load='5yec' size='340' side='right'caption='[[5yec]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
<StructureSection load='5yec' size='340' side='right'caption='[[5yec]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5yec]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YEC FirstGlance]. <br>
<table><tr><td colspan='2'>[[5yec]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YEC FirstGlance]. <br>
</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.147&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yec OCA], [http://pdbe.org/5yec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yec RCSB], [http://www.ebi.ac.uk/pdbsum/5yec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yec ProSAT]</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=MG:MAGNESIUM+ION'>MG</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=5yec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yec OCA], [https://pdbe.org/5yec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yec RCSB], [https://www.ebi.ac.uk/pdbsum/5yec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yec ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ATG7_YEAST ATG7_YEAST]] E1-like activating enzyme involved in the 2 ubiquitin-like systems required for cytoplasm to vacuole transport (Cvt) and autophagy. Activates ATG12 for its conjugation with ATG5 and ATG8 for its conjugation with phosphatidylethanolamine. Both systems are needed for the ATG8 association to Cvt vesicles and autophagosomes membranes.<ref>PMID:9759731</ref> <ref>PMID:8224160</ref> <ref>PMID:7593182</ref> <ref>PMID:10233148</ref> <ref>PMID:10233150</ref> <ref>PMID:11100732</ref> <ref>PMID:11149920</ref> <ref>PMID:12965207</ref> <ref>PMID:15277523</ref> [[http://www.uniprot.org/uniprot/ATG8_YEAST ATG8_YEAST]] Involved in cytoplasm to vacuole transport (Cvt) vesicles and autophagosomes formation. With ATG4, may mediate the delivery of the vesicles and autophagosomes to the vacuole via the microtubule cytoskeleton. Participates also in membrane fusion events that take place in the early secretory pathway.<ref>PMID:8224160</ref> <ref>PMID:7593182</ref> <ref>PMID:9649430</ref> <ref>PMID:10525546</ref> <ref>PMID:10681575</ref> <ref>PMID:10837468</ref> <ref>PMID:11038174</ref> <ref>PMID:11100732</ref> <ref>PMID:11149920</ref> 
[https://www.uniprot.org/uniprot/ATG7_YEAST ATG7_YEAST] E1-like activating enzyme involved in the 2 ubiquitin-like systems required for cytoplasm to vacuole transport (Cvt) and autophagy. Activates ATG12 for its conjugation with ATG5 and ATG8 for its conjugation with phosphatidylethanolamine. Both systems are needed for the ATG8 association to Cvt vesicles and autophagosomes membranes.<ref>PMID:9759731</ref> <ref>PMID:8224160</ref> <ref>PMID:7593182</ref> <ref>PMID:10233148</ref> <ref>PMID:10233150</ref> <ref>PMID:11100732</ref> <ref>PMID:11149920</ref> <ref>PMID:12965207</ref> <ref>PMID:15277523</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Atg8 is a unique ubiquitin-like protein that is covalently conjugated with a phosphatidylethanolamine through reactions similar to ubiquitination and plays essential roles in autophagy. Atg7 is the E1 enzyme for Atg8, and it activates the C-terminal Gly116 of Atg8 using ATP. Here, we report the crystal structure of Atg8 bound to the C-terminal domain of Atg7 in an unprecedented mode. Atg8 neither contacts with the central beta-sheet nor binds to the catalytic site of Atg7, both of which were observed in previously reported Atg7-Atg8 structures. Instead, Atg8 binds to the C-terminal alpha-helix and crossover loop, thereby changing the autoinhibited conformation of the crossover loop observed in the free Atg7 structure into a short helix and a disordered loop. Mutational analyses suggested that this interaction mode is important for the activation reaction. We propose that Atg7 recognizes Atg8 through multiple steps, which would be necessary to induce a conformational change in Atg7 that is optimal for the activation reaction.
 
Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition.,Yamaguchi M, Satoo K, Suzuki H, Fujioka Y, Ohsumi Y, Inagaki F, Noda NN J Mol Biol. 2018 Feb 2;430(3):249-257. doi: 10.1016/j.jmb.2017.12.002. Epub 2017 , Dec 10. PMID:29237558<ref>PMID:29237558</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5yec" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Autophagy-related protein 3D structures|Autophagy-related protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Noda, N N]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Satoo, K]]
[[Category: Noda NN]]
[[Category: Yamaguchi, M]]
[[Category: Satoo K]]
[[Category: Autophagy]]
[[Category: Yamaguchi M]]
[[Category: E1 enzyme]]
[[Category: Metal binding protein]]
[[Category: Protein transport-metal binding protein complex]]
[[Category: Ubiquitin-like protein]]
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