2lpu: Difference between revisions

Revision as of 09:07, 14 June 2023

Solution structures of KmAtg10

Structural highlights

2lpu is a 1 chain structure with sequence from Kluyveromyces marxianus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ATG10_KLUMD E2-like enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy and nucleophagy (PubMed:26442587, PubMed:22682742). Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5 (PubMed:22682742). ATG12 conjugation to ATG5 is required for proper localization of ATG8 to the preautophagosomal structure (PAS) (By similarity). Likely serves as an ATG5-recognition molecule (By similarity).[UniProtKB:Q07879]^[1] ^[2]

Publication Abstract from PubMed

The Atg12-Atg5 conjugate, which is formed by an ubiquitin-like conjugation system, is essential to autophagosome formation, a central event in autophagy. Despite its importance, the molecular mechanism of the Atg12-Atg5 conjugate formation has not been elucidated. Here, we report the solution and crystal structures of Atg10 and Atg5 homologs from Kluyveromyces marxianus (Km), a thermotolerant yeast. KmAtg10 comprises an E2-core fold with characteristic accessories, including two beta strands, whereas KmAtg5 has two ubiquitin-like domains and a helical domain. The nuclear magnetic resonance experiments, mutational analyses, and crosslinking experiments showed that KmAtg10 directly recognizes KmAtg5, especially its C-terminal ubiquitin-like domain, by its characteristic two beta strands. Kinetic analysis suggests that Tyr56 and Asn114 of KmAtg10 may place the side chain of KmAtg5 Lys145 into the optimal orientation for its conjugation reaction with Atg12. These structural features enable Atg10 to mediate the formation of the Atg12-Atg5 conjugate without a specific E3 enzyme.

Structural insights into atg10-mediated formation of the autophagy-essential atg12-atg5 conjugate.,Yamaguchi M, Noda NN, Yamamoto H, Shima T, Kumeta H, Kobashigawa Y, Akada R, Ohsumi Y, Inagaki F Structure. 2012 Jul 3;20(7):1244-54. Epub 2012 Jun 7. PMID:22682742^[3]

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

References

↑ Yamaguchi M, Noda NN, Yamamoto H, Shima T, Kumeta H, Kobashigawa Y, Akada R, Ohsumi Y, Inagaki F. Structural insights into atg10-mediated formation of the autophagy-essential atg12-atg5 conjugate. Structure. 2012 Jul 3;20(7):1244-54. Epub 2012 Jun 7. PMID:22682742 doi:10.1016/j.str.2012.04.018
↑ Yamamoto H, Shima T, Yamaguchi M, Mochizuki Y, Hoshida H, Kakuta S, Kondo-Kakuta C, Noda NN, Inagaki F, Itoh T, Akada R, Ohsumi Y. The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy. J Biol Chem. 2015 Dec 4;290(49):29506-18. PMID:26442587 doi:10.1074/jbc.M115.684233
↑ Yamaguchi M, Noda NN, Yamamoto H, Shima T, Kumeta H, Kobashigawa Y, Akada R, Ohsumi Y, Inagaki F. Structural insights into atg10-mediated formation of the autophagy-essential atg12-atg5 conjugate. Structure. 2012 Jul 3;20(7):1244-54. Epub 2012 Jun 7. PMID:22682742 doi:10.1016/j.str.2012.04.018

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Yamaguchi M, Noda NN, Yamamoto H, Shima T, Kumeta H, Kobashigawa Y, Akada R, Ohsumi Y, Inagaki F. Structural insights into atg10-mediated formation of the autophagy-essential atg12-atg5 conjugate. Structure. 2012 Jul 3;20(7):1244-54. Epub 2012 Jun 7. PMID:22682742 doi:10.1016/j.str.2012.04.018

[2] Yamamoto H, Shima T, Yamaguchi M, Mochizuki Y, Hoshida H, Kakuta S, Kondo-Kakuta C, Noda NN, Inagaki F, Itoh T, Akada R, Ohsumi Y. The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy. J Biol Chem. 2015 Dec 4;290(49):29506-18. PMID:26442587 doi:10.1074/jbc.M115.684233

[3] Yamaguchi M, Noda NN, Yamamoto H, Shima T, Kumeta H, Kobashigawa Y, Akada R, Ohsumi Y, Inagaki F. Structural insights into atg10-mediated formation of the autophagy-essential atg12-atg5 conjugate. Structure. 2012 Jul 3;20(7):1244-54. Epub 2012 Jun 7. PMID:22682742 doi:10.1016/j.str.2012.04.018

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[2]

[3]

@@ Line 1: / Line 1: @@
 ==Solution structures of KmAtg10==
-<StructureSection load='2lpu' size='340' side='right'caption='[[2lpu]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2lpu' size='340' side='right'caption='[[2lpu]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2lpu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_712 Cbs 712]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LPU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2lpu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_marxianus Kluyveromyces marxianus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LPU FirstGlance]. <br>
 </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=2lpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lpu OCA], [https://pdbe.org/2lpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lpu RCSB], [https://www.ebi.ac.uk/pdbsum/2lpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lpu ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ATG10_KLUMD ATG10_KLUMD] E2-like enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy and nucleophagy (PubMed:26442587, PubMed:22682742). Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5 (PubMed:22682742). ATG12 conjugation to ATG5 is required for proper localization of ATG8 to the preautophagosomal structure (PAS) (By similarity). Likely serves as an ATG5-recognition molecule (By similarity).[UniProtKB:Q07879]<ref>PMID:22682742</ref> <ref>PMID:26442587</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Cbs 712]]
+[[Category: Kluyveromyces marxianus]]
 [[Category: Large Structures]]
-[[Category: Akada, R]]
+[[Category: Akada R]]
-[[Category: Inagaki, F]]
+[[Category: Inagaki F]]
-[[Category: Kobashigawa, Y]]
+[[Category: Kobashigawa Y]]
-[[Category: Kumeta, H]]
+[[Category: Kumeta H]]
-[[Category: Noda, N N]]
+[[Category: Noda NN]]
-[[Category: Ohsumi, Y]]
+[[Category: Ohsumi Y]]
-[[Category: Shima, T]]
+[[Category: Shima T]]
-[[Category: Yamaguchi, M]]
+[[Category: Yamaguchi M]]
-[[Category: Yamamoto, H]]
+[[Category: Yamamoto H]]
-[[Category: Atg10]]
-[[Category: Autophagy]]
-[[Category: E2-like]]
-[[Category: Protein transport]]
-[[Category: Proteolysis]]

2lpu: Difference between revisions

Revision as of 09:07, 14 June 2023

Solution structures of KmAtg10

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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