3vh3: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3vh3]] is a 2 chain structure with sequence 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=3VH3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VH3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3vh3]] is a 2 chain structure with sequence 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=3VH3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VH3 FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vh1|3vh1]], [[3vh2|3vh2]], [[3vh4|3vh4]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vh1|3vh1]], [[3vh2|3vh2]], [[3vh4|3vh4]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATG7, APG7, CVT2, YHR171W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATG7, APG7, CVT2, YHR171W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vh3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vh3 RCSB], [http://www.ebi.ac.uk/pdbsum/3vh3 PDBsum]</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=3vh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vh3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vh3 RCSB], [http://www.ebi.ac.uk/pdbsum/3vh3 PDBsum]</span></td></tr>
<table>
</table>
== 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> 
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 14: Line 16:
Structural basis of Atg8 activation by a homodimeric E1, Atg7.,Noda NN, Satoo K, Fujioka Y, Kumeta H, Ogura K, Nakatogawa H, Ohsumi Y, Inagaki F Mol Cell. 2011 Nov 4;44(3):462-75. PMID:22055191<ref>PMID:22055191</ref>
Structural basis of Atg8 activation by a homodimeric E1, Atg7.,Noda NN, Satoo K, Fujioka Y, Kumeta H, Ogura K, Nakatogawa H, Ohsumi Y, Inagaki F Mol Cell. 2011 Nov 4;44(3):462-75. PMID:22055191<ref>PMID:22055191</ref>


From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
== References ==
== References ==
Line 21: Line 23:
</StructureSection>
</StructureSection>
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Inagaki, F.]]
[[Category: Inagaki, F]]
[[Category: Noda, N N.]]
[[Category: Noda, N N]]
[[Category: Satoo, K.]]
[[Category: Satoo, K]]
[[Category: Autophagy]]
[[Category: Autophagy]]
[[Category: E1]]
[[Category: E1]]
[[Category: Metal binding protein-protein transport complex]]
[[Category: Metal binding protein-protein transport complex]]
[[Category: Zinc binding]]
[[Category: Zinc binding]]

Revision as of 14:48, 25 December 2014

Crystal structure of Atg7CTD-Atg8 complexCrystal structure of Atg7CTD-Atg8 complex

Structural highlights

3vh3 is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:ATG7, APG7, CVT2, YHR171W (Saccharomyces cerevisiae), ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 (Saccharomyces cerevisiae)
Resources:FirstGlance, OCA, RCSB, PDBsum

Function

[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.[1] [2] [3] [4] [5] [6] [7] [8] [9] [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.[10] [11] [12] [13] [14] [15] [16] [17] [18]

Publication Abstract from PubMed

E1 enzymes activate ubiquitin-like proteins and transfer them to cognate E2 enzymes. Atg7, a noncanonical E1, activates two ubiquitin-like proteins, Atg8 and Atg12, and plays a crucial role in autophagy. Here, we report crystal structures of full-length Atg7 and its C-terminal domain bound to Atg8 and MgATP, as well as a solution structure of Atg8 bound to the extreme C-terminal domain (ECTD) of Atg7. The unique N-terminal domain (NTD) of Atg7 is responsible for Atg3 (E2) binding, whereas its C-terminal domain is comprised of a homodimeric adenylation domain (AD) and ECTD. The structural and biochemical data demonstrate that Atg8 is initially recognized by the C-terminal tail of ECTD and is then transferred to an AD, where the Atg8 C terminus is attacked by the catalytic cysteine to form a thioester bond. Atg8 is then transferred via a trans mechanism to the Atg3 bound to the NTD of the opposite protomer within a dimer.

Structural basis of Atg8 activation by a homodimeric E1, Atg7.,Noda NN, Satoo K, Fujioka Y, Kumeta H, Ogura K, Nakatogawa H, Ohsumi Y, Inagaki F Mol Cell. 2011 Nov 4;44(3):462-75. PMID:22055191[19]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ 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
  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. ↑ Harding TM, Morano KA, Scott SV, Klionsky DJ. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol. 1995 Nov;131(3):591-602. PMID:7593182
  4. ↑ Kim J, Dalton VM, Eggerton KP, Scott SV, Klionsky DJ. Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Mol Biol Cell. 1999 May;10(5):1337-51. PMID:10233148
  5. ↑ Tanida I, Mizushima N, Kiyooka M, Ohsumi M, Ueno T, Ohsumi Y, Kominami E. Apg7p/Cvt2p: A novel protein-activating enzyme essential for autophagy. Mol Biol Cell. 1999 May;10(5):1367-79. PMID:10233150
  6. ↑ 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
  7. ↑ 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
  8. ↑ Yamazaki-Sato H, Tanida I, Ueno T, Kominami E. The carboxyl terminal 17 amino acids within Apg7 are essential for Apg8 lipidation, but not for Apg12 conjugation. FEBS Lett. 2003 Sep 11;551(1-3):71-7. PMID:12965207
  9. ↑ 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
  10. ↑ 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
  11. ↑ Harding TM, Morano KA, Scott SV, Klionsky DJ. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol. 1995 Nov;131(3):591-602. PMID:7593182
  12. ↑ Lang T, Schaeffeler E, Bernreuther D, Bredschneider M, Wolf DH, Thumm M. Aut2p and Aut7p, two novel microtubule-associated proteins are essential for delivery of autophagic vesicles to the vacuole. EMBO J. 1998 Jul 1;17(13):3597-607. PMID:9649430 doi:10.1093/emboj/17.13.3597
  13. ↑ Kirisako T, Baba M, Ishihara N, Miyazawa K, Ohsumi M, Yoshimori T, Noda T, Ohsumi Y. Formation process of autophagosome is traced with Apg8/Aut7p in yeast. J Cell Biol. 1999 Oct 18;147(2):435-46. PMID:10525546
  14. ↑ Huang WP, Scott SV, Kim J, Klionsky DJ. The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. J Biol Chem. 2000 Feb 25;275(8):5845-51. PMID:10681575
  15. ↑ Legesse-Miller A, Sagiv Y, Glozman R, Elazar Z. Aut7p, a soluble autophagic factor, participates in multiple membrane trafficking processes. J Biol Chem. 2000 Oct 20;275(42):32966-73. PMID:10837468 doi:10.1074/jbc.M000917200
  16. ↑ Kirisako T, Ichimura Y, Okada H, Kabeya Y, Mizushima N, Yoshimori T, Ohsumi M, Takao T, Noda T, Ohsumi Y. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J Cell Biol. 2000 Oct 16;151(2):263-76. PMID:11038174
  17. ↑ 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
  18. ↑ 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
  19. ↑ Noda NN, Satoo K, Fujioka Y, Kumeta H, Ogura K, Nakatogawa H, Ohsumi Y, Inagaki F. Structural basis of Atg8 activation by a homodimeric E1, Atg7. Mol Cell. 2011 Nov 4;44(3):462-75. PMID:22055191 doi:10.1016/j.molcel.2011.08.035

3vh3, resolution 2.00Å

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