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[[Image:2dym.jpg|left|200px]]<br /><applet load="2dym" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2dym, resolution 2.20&Aring;" />
'''The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex'''<br />


==Overview==
==The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex==
Atg5 is covalently modified with a ubiquitin-like modifier, Atg12, and the, Atg12-Atg5 conjugate further forms a complex with the multimeric protein, Atg16. The Atg12-Atg5.Atg16 multimeric complex plays an essential role in, autophagy, the bulk degradation system conserved in all eukaryotes. We, have reported here the crystal structure of Atg5 complexed with the, N-terminal region of Atg16 at 1.97A resolution. Atg5 comprises two, ubiquitin-like domains that flank a helix-rich domain. The N-terminal, region of Atg16 has a helical structure and is bound to the groove formed, by these three domains. In vitro analysis showed that Arg-35 and Phe-46 of, Atg16 are crucial for the interaction. Atg16, with a mutation at these, residues, failed to localize to the pre-autophagosomal structure and could, not restore autophagy in Atg16-deficient yeast strains. Furthermore, these, Atg16 mutants could not restore a severe reduction in the formation of the, Atg8-phosphatidylethanolamine conjugate, another essential factor for, autophagy, in Atg16-deficient strains under starvation conditions. These, results taken together suggest that the direct interaction between Atg5, and Atg16 is crucial to the performance of their roles in autophagy.
<StructureSection load='2dym' size='340' side='right'caption='[[2dym]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2dym]] is a 8 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=2DYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DYM 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]] 2.2&#8491;</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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [https://pdbe.org/2dym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [https://www.ebi.ac.uk/pdbsum/2dym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dym ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ATG5_YEAST ATG5_YEAST] Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.<ref>PMID:8921905</ref> <ref>PMID:8224160</ref> <ref>PMID:9759731</ref> <ref>PMID:10406794</ref> <ref>PMID:10712513</ref> <ref>PMID:11149920</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/2dym_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=2dym ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2DYM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA].
*[[Autophagy-related protein 3D structures|Autophagy-related protein 3D structures]]
 
== References ==
==Reference==
<references/>
Structure of Atg5.Atg16, a complex essential for autophagy., Matsushita M, Suzuki NN, Obara K, Fujioka Y, Ohsumi Y, Inagaki F, J Biol Chem. 2007 Mar 2;282(9):6763-72. Epub 2006 Dec 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17192262 17192262]
__TOC__
[[Category: Protein complex]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Inagaki, F.]]
[[Category: Inagaki F]]
[[Category: Matsushita, M.]]
[[Category: Matsushita M]]
[[Category: Suzuki, N.N.]]
[[Category: Suzuki NN]]
[[Category: herix-bundle]]
[[Category: ubiquitin-fold]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:37:23 2008''

Latest revision as of 16:48, 13 March 2024

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complexThe crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex

Structural highlights

2dym is a 8 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 2.2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ATG5_YEAST Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.[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. ↑ Kametaka S, Matsuura A, Wada Y, Ohsumi Y. Structural and functional analyses of APG5, a gene involved in autophagy in yeast. Gene. 1996 Oct 31;178(1-2):139-43. PMID:8921905
  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. ↑ Mizushima N, Noda T, Yoshimori T, Tanaka Y, Ishii T, George MD, Klionsky DJ, Ohsumi M, Ohsumi Y. A protein conjugation system essential for autophagy. Nature. 1998 Sep 24;395(6700):395-8. PMID:9759731 doi:10.1038/26506
  4. ↑ Mizushima N, Noda T, Ohsumi Y. Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. EMBO J. 1999 Jul 15;18(14):3888-96. PMID:10406794 doi:10.1093/emboj/18.14.3888
  5. ↑ George MD, Baba M, Scott SV, Mizushima N, Garrison BS, Ohsumi Y, Klionsky DJ. Apg5p functions in the sequestration step in the cytoplasm-to-vacuole targeting and macroautophagy pathways. Mol Biol Cell. 2000 Mar;11(3):969-82. PMID:10712513
  6. ↑ 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

2dym, resolution 2.20Å

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