2dyt: Difference between revisions

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New page: left|200px<br /><applet load="2dyt" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dyt, resolution 2.50Å" /> '''The crystal structur...
 
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[[Image:2dyt.gif|left|200px]]<br /><applet load="2dyt" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2dyt, resolution 2.50&Aring;" />
'''The crystal structure of Saccharomyces cerevisiae Atg3'''<br />


==Overview==
==The crystal structure of Saccharomyces cerevisiae Atg3==
Atg3 is an E2-like enzyme that catalyzes the conjugation of Atg8 and, phosphatidylethanolamine (PE). The Atg8-PE conjugate is essential for, autophagy, which is the bulk degradation process of cytoplasmic components, by the vacuolar/lysosomal system. We report here the crystal structure of, Saccharomyces cerevisiae Atg3 at 2.5-A resolution. Atg3 has an, alpha/beta-fold, and its core region is topologically similar to canonical, E2 enzymes. Atg3 has two regions inserted in the core region, one of which, consists of approximately 80 residues and has a random coil structure in, solution and another with a long alpha-helical structure that protrudes, from the core region as far as 30 A. In vivo and in vitro analyses, suggested that the former region is responsible for binding Atg7, an, E1-like enzyme, and that the latter is responsible for binding Atg8. A, sulfate ion was bound near the catalytic cysteine of Atg3, suggesting a, possible binding site for the phosphate moiety of PE. The structure of, Atg3 provides a molecular basis for understanding the unique lipidation, reaction that Atg3 carries out.
<StructureSection load='2dyt' size='340' side='right'caption='[[2dyt]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2dyt]] is a 1 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=2DYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DYT FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=2dyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dyt OCA], [https://pdbe.org/2dyt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dyt RCSB], [https://www.ebi.ac.uk/pdbsum/2dyt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dyt ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ATG3_YEAST ATG3_YEAST] E2 conjugating enzyme responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8. This step is required for the membrane association of ATG8. The formation of the ATG8-phosphatidylethanolamine conjugate is essential for autophagy and for the cytoplasm to vacuole transport (Cvt).<ref>PMID:9023185</ref> <ref>PMID:8224160</ref> <ref>PMID:8050581</ref> <ref>PMID:11100732</ref> <ref>PMID:11149920</ref> <ref>PMID:15277523</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/2dyt_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dyt ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2DYT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DYT OCA].
*[[Autophagy-related protein 3D structures|Autophagy-related protein 3D structures]]
 
== References ==
==Reference==
<references/>
The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation., Yamada Y, Suzuki NN, Hanada T, Ichimura Y, Kumeta H, Fujioka Y, Ohsumi Y, Inagaki F, J Biol Chem. 2007 Mar 16;282(11):8036-43. Epub 2007 Jan 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17227760 17227760]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Inagaki F]]
[[Category: Inagaki, F.]]
[[Category: Suzuki NN]]
[[Category: Suzuki, N.N.]]
[[Category: Yamada Y]]
[[Category: Yamada, Y.]]
[[Category: SO4]]
[[Category: e2 fold]]
[[Category: ligase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:52:10 2007''

Latest revision as of 16:48, 13 March 2024

The crystal structure of Saccharomyces cerevisiae Atg3The crystal structure of Saccharomyces cerevisiae Atg3

Structural highlights

2dyt is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ATG3_YEAST E2 conjugating enzyme responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8. This step is required for the membrane association of ATG8. The formation of the ATG8-phosphatidylethanolamine conjugate is essential for autophagy and for the cytoplasm to vacuole transport (Cvt).[1] [2] [3] [4] [5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Schlumpberger M, Schaeffeler E, Straub M, Bredschneider M, Wolf DH, Thumm M. AUT1, a gene essential for autophagocytosis in the yeast Saccharomyces cerevisiae. J Bacteriol. 1997 Feb;179(4):1068-76. PMID:9023185
  2. ↑ Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993 Oct 25;333(1-2):169-74. PMID:8224160
  3. ↑ Thumm M, Egner R, Koch B, Schlumpberger M, Straub M, Veenhuis M, Wolf DH. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett. 1994 Aug 1;349(2):275-80. PMID:8050581
  4. ↑ Ichimura Y, Kirisako T, Takao T, Satomi Y, Shimonishi Y, Ishihara N, Mizushima N, Tanida I, Kominami E, Ohsumi M, Noda T, Ohsumi Y. A ubiquitin-like system mediates protein lipidation. Nature. 2000 Nov 23;408(6811):488-92. PMID:11100732 doi:10.1038/35044114
  5. ↑ Kim J, Huang WP, Klionsky DJ. Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex. J Cell Biol. 2001 Jan 8;152(1):51-64. PMID:11149920
  6. ↑ Ichimura Y, Imamura Y, Emoto K, Umeda M, Noda T, Ohsumi Y. In vivo and in vitro reconstitution of Atg8 conjugation essential for autophagy. J Biol Chem. 2004 Sep 24;279(39):40584-92. Epub 2004 Jul 23. PMID:15277523 doi:10.1074/jbc.M405860200

2dyt, resolution 2.50Å

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