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3w1s

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Revision as of 05:18, 3 August 2022

Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16

Structural highlights

3w1s is a 3 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	APG5, ATG5, Atg5(amino acids 1-284), P2601, YPL149W (Baker's yeast), APG15, APG16, ATG16, Atg16(amino acids 1-46), CVT11, SAP18, YM8520.08C, YMR159C (Baker's yeast), APG12, ATG12, Atg12(amino acids 100-186), YBR1506, YBR217W (Baker's yeast)
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] [ATG12_YEAST] Ubiquitin-like protein involved in cytoplasm to vacuole transport (Cvt), autophagy vesicles formation, mitophagy, and nucleophagy. Conjugation with ATG5 through an ubiquitin-like conjugating system involving also ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme, is essential for its function. The ATG12-ATG5 conjugate acts as an E3-like enzyme which is required for lipidation of ATG8 and ATG8 association to the vesicle membranes. ATG12-ATG5 rearranges the ATG3 catalytic center and enhances its E2 activity.^[7] ^[8] ^[9] [ATG16_YEAST] Stabilizes the ATG5-ATG12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. Required for ATG8 localization to the pre-autophagosomal structure.^[10] ^[11] ^[12] ^[13] ^[14]

Publication Abstract from PubMed

Atg12 is conjugated to Atg5 through enzymatic reactions similar to ubiquitination. The Atg12-Atg5 conjugate functions as an E3-like enzyme to promote lipidation of Atg8, whereas lipidated Atg8 has essential roles in both autophagosome formation and selective cargo recognition during autophagy. However, the molecular role of Atg12 modification in these processes has remained elusive. Here, we report the crystal structure of the Atg12-Atg5 conjugate. In addition to the isopeptide linkage, Atg12 forms hydrophobic and hydrophilic interactions with Atg5, thereby fixing its position on Atg5. Structural comparison with unmodified Atg5 and mutational analyses showed that Atg12 modification neither induces a conformational change in Atg5 nor creates a functionally important architecture. Rather, Atg12 functions as a binding module for Atg3, the E2 enzyme for Atg8, thus endowing Atg5 with the ability to interact with Atg3 to facilitate Atg8 lipidation.

Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation.,Noda NN, Fujioka Y, Hanada T, Ohsumi Y, Inagaki F EMBO Rep. 2012 Dec 14. doi: 10.1038/embor.2012.208. PMID:23238393^[15]

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

References

↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ Harding TM, Hefner-Gravink A, Thumm M, Klionsky DJ. Genetic and phenotypic overlap between autophagy and the cytoplasm to vacuole protein targeting pathway. J Biol Chem. 1996 Jul 26;271(30):17621-4. PMID:8663607
↑ 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
↑ Suzuki K, Kirisako T, Kamada Y, Mizushima N, Noda T, Ohsumi Y. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J. 2001 Nov 1;20(21):5971-81. PMID:11689437 doi:10.1093/emboj/20.21.5971
↑ Kuma A, Mizushima N, Ishihara N, Ohsumi Y. Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. J Biol Chem. 2002 May 24;277(21):18619-25. Epub 2002 Mar 15. PMID:11897782 doi:10.1074/jbc.M111889200
↑ Noda NN, Fujioka Y, Hanada T, Ohsumi Y, Inagaki F. Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation. EMBO Rep. 2012 Dec 14. doi: 10.1038/embor.2012.208. PMID:23238393 doi:10.1038/embor.2012.208

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3w1s"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16==
-<StructureSection load='3w1s' size='340' side='right' caption='[[3w1s]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='3w1s' size='340' side='right'caption='[[3w1s]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3w1s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W1S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3w1s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W1S FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APG5, ATG5, Atg5(amino acids 1-284), P2601, YPL149W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), APG15, APG16, ATG16, Atg16(amino acids 1-46), CVT11, SAP18, YM8520.08C, YMR159C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), APG12, ATG12, Atg12(amino acids 100-186), YBR1506, YBR217W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APG5, ATG5, Atg5(amino acids 1-284), P2601, YPL149W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), APG15, APG16, ATG16, Atg16(amino acids 1-46), CVT11, SAP18, YM8520.08C, YMR159C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), APG12, ATG12, Atg12(amino acids 100-186), YBR1506, YBR217W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=3w1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1s OCA], [http://pdbe.org/3w1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w1s RCSB], [http://www.ebi.ac.uk/pdbsum/3w1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1s ProSAT]</span></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=3w1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1s OCA], [https://pdbe.org/3w1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w1s RCSB], [https://www.ebi.ac.uk/pdbsum/3w1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1s ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>  [[http://www.uniprot.org/uniprot/ATG12_YEAST ATG12_YEAST]] Ubiquitin-like protein involved in cytoplasm to vacuole transport (Cvt), autophagy vesicles formation, mitophagy, and nucleophagy. Conjugation with ATG5 through an ubiquitin-like conjugating system involving also ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme, is essential for its function. The ATG12-ATG5 conjugate acts as an E3-like enzyme which is required for lipidation of ATG8 and ATG8 association to the vesicle membranes. ATG12-ATG5 rearranges the ATG3 catalytic center and enhances its E2 activity.<ref>PMID:9759731</ref> <ref>PMID:8224160</ref> <ref>PMID:11149920</ref>  [[http://www.uniprot.org/uniprot/ATG16_YEAST ATG16_YEAST]] Stabilizes the ATG5-ATG12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. Required for ATG8 localization to the pre-autophagosomal structure.<ref>PMID:8224160</ref> <ref>PMID:8663607</ref> <ref>PMID:10406794</ref> <ref>PMID:11689437</ref> <ref>PMID:11897782</ref>
+[[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>  [[https://www.uniprot.org/uniprot/ATG12_YEAST ATG12_YEAST]] Ubiquitin-like protein involved in cytoplasm to vacuole transport (Cvt), autophagy vesicles formation, mitophagy, and nucleophagy. Conjugation with ATG5 through an ubiquitin-like conjugating system involving also ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme, is essential for its function. The ATG12-ATG5 conjugate acts as an E3-like enzyme which is required for lipidation of ATG8 and ATG8 association to the vesicle membranes. ATG12-ATG5 rearranges the ATG3 catalytic center and enhances its E2 activity.<ref>PMID:9759731</ref> <ref>PMID:8224160</ref> <ref>PMID:11149920</ref>  [[https://www.uniprot.org/uniprot/ATG16_YEAST ATG16_YEAST]] Stabilizes the ATG5-ATG12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. Required for ATG8 localization to the pre-autophagosomal structure.<ref>PMID:8224160</ref> <ref>PMID:8663607</ref> <ref>PMID:10406794</ref> <ref>PMID:11689437</ref> <ref>PMID:11897782</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 20: @@
 ==See Also==
-*[[Autophagy-related protein|Autophagy-related protein]]
+*[[Autophagy-related protein 3D structures|Autophagy-related protein 3D structures]]
 == References ==
 <references/>
@@ Line 26: / Line 26: @@
 </StructureSection>
 [[Category: Baker's yeast]]
+[[Category: Large Structures]]
 [[Category: Fujioka, Y]]
 [[Category: Hanada, T]]

3w1s

From Proteopedia

Revision as of 05:18, 3 August 2022

Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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