2kzb

From Proteopedia

(Difference between revisions)

Current revision

Solution structure of alpha-mannosidase binding domain of Atg19

Structural highlights

2kzb is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ATG19_YEAST Cargo-receptor protein involved in the cytoplasm to vacuole transport (Cvt) and in autophagy. Recognizes cargo proteins, such as APE4, LAP3, LAP4 and AMS1 and delivers them to the pre-autophagosomal structure for eventual engulfment by the autophagosome and targeting to the vacuole. Involved in the organization of the preautophagosomal structure (PAS). ATG19 association with cargo protein is required to localize ATG11 to the PAS. Also involved in endoplasmic reticulum-specific autophagic process, in selective removal of ER-associated degradation (ERAD) substrates, and is essential for the survival of cells subjected to severe ER stress. Plays also a role in regulation of filamentous growth.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16]

Publication Abstract from PubMed

In the yeast Saccharomyces cerevisiae, a precursor form of aminopeptidase I (prApe1) and alpha-mannosidase (Ams1) are selectively transported to the vacuole through the cytoplasm-to-vacuole targeting pathway under vegetative conditions and through autophagy under starvation conditions. Atg19 plays a central role in these processes by linking Ams1 and prApe1 to Atg8 and Atg11. However, little is known about the molecular mechanisms of cargo recognition by Atg19. Here, we report structural and functional analyses of Atg19 and its paralog, Atg34. A protease-resistant domain was identified in the C-terminal region of Atg19, which was also conserved in Atg34. In vitro pulldown assays showed that the C-terminal domains of both Atg19 and Atg34 are responsible for Ams1 binding; these domains are hereafter referred to as Ams1-binding domains (ABDs). The transport of Ams1, but not prApe1, was blocked in atg19Deltaatg34Delta cells expressing Atg19(DeltaABD), indicating that ABD is specifically required for Ams1 transport. We then determined the solution structures of the ABDs of Atg19 and Atg34 using NMR spectroscopy. Both ABD structures have a canonical immunoglobulin fold consisting of eight beta-strands with highly conserved loops clustered at one side of the fold. These facts, together with the results of a mutational analysis, suggest that ABD recognizes Ams1 using these conserved loops.

Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34.,Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F J Biol Chem. 2010 Sep 24;285(39):30026-33. Epub 2010 Jul 21. PMID:20659891^[17]

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

References

↑ Leber R, Silles E, Sandoval IV, Mazon MJ. Yol082p, a novel CVT protein involved in the selective targeting of aminopeptidase I to the yeast vacuole. J Biol Chem. 2001 Aug 3;276(31):29210-7. Epub 2001 May 29. PMID:11382752 doi:http://dx.doi.org/10.1074/jbc.M101438200
↑ Scott SV, Guan J, Hutchins MU, Kim J, Klionsky DJ. Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway. Mol Cell. 2001 Jun;7(6):1131-41. PMID:11430817
↑ Suzuki K, Kamada Y, Ohsumi Y. Studies of cargo delivery to the vacuole mediated by autophagosomes in Saccharomyces cerevisiae. Dev Cell. 2002 Dec;3(6):815-24. PMID:12479807
↑ Shintani T, Huang WP, Stromhaug PE, Klionsky DJ. Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway. Dev Cell. 2002 Dec;3(6):825-37. PMID:12479808
↑ Shintani T, Klionsky DJ. Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway. J Biol Chem. 2004 Jul 16;279(29):29889-94. Epub 2004 May 11. PMID:15138258 doi:http://dx.doi.org/10.1074/jbc.M404399200
↑ Cebollero E, Carrascosa AV, Gonzalez R. Evidence for yeast autophagy during simulation of sparkling wine aging: a reappraisal of the mechanism of yeast autolysis in wine. Biotechnol Prog. 2005 Mar-Apr;21(2):614-6. PMID:15801807 doi:http://dx.doi.org/10.1021/bp049708y
↑ Baxter BK, Abeliovich H, Zhang X, Stirling AG, Burlingame AL, Goldfarb DS. Atg19p ubiquitination and the cytoplasm to vacuole trafficking pathway in yeast. J Biol Chem. 2005 Nov 25;280(47):39067-76. Epub 2005 Sep 26. PMID:16186126 doi:http://dx.doi.org/10.1074/jbc.M508064200
↑ Yorimitsu T, Klionsky DJ. Atg11 links cargo to the vesicle-forming machinery in the cytoplasm to vacuole targeting pathway. Mol Biol Cell. 2005 Apr;16(4):1593-605. Epub 2005 Jan 19. PMID:15659643 doi:http://dx.doi.org/10.1091/mbc.E04-11-1035
↑ Bernales S, McDonald KL, Walter P. Autophagy counterbalances endoplasmic reticulum expansion during the unfolded protein response. PLoS Biol. 2006 Nov;4(12):e423. PMID:17132049 doi:http://dx.doi.org/10.1371/journal.pbio.0040423
↑ Ma J, Jin R, Dobry CJ, Lawson SK, Kumar A. Overexpression of autophagy-related genes inhibits yeast filamentous growth. Autophagy. 2007 Nov-Dec;3(6):604-9. Epub 2007 Jul 24. PMID:17700056
↑ Chang CY, Huang WP. Atg19 mediates a dual interaction cargo sorting mechanism in selective autophagy. Mol Biol Cell. 2007 Mar;18(3):919-29. Epub 2006 Dec 27. PMID:17192412 doi:http://dx.doi.org/10.1091/mbc.E06-08-0683
↑ Mazon MJ, Eraso P, Portillo F. Efficient degradation of misfolded mutant Pma1 by endoplasmic reticulum-associated degradation requires Atg19 and the Cvt/autophagy pathway. Mol Microbiol. 2007 Feb;63(4):1069-77. PMID:17238920 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05580.x
↑ Kageyama T, Suzuki K, Ohsumi Y. Lap3 is a selective target of autophagy in yeast, Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2009 Jan 16;378(3):551-7. doi:, 10.1016/j.bbrc.2008.11.084. Epub 2008 Dec 4. PMID:19061865 doi:http://dx.doi.org/10.1016/j.bbrc.2008.11.084
↑ Kario E, Amar N, Elazar Z, Navon A. A new autophagy-related checkpoint in the degradation of an ERAD-M target. J Biol Chem. 2011 Apr 1;286(13):11479-91. doi: 10.1074/jbc.M110.177618. Epub 2011, Jan 12. PMID:21228276 doi:http://dx.doi.org/10.1074/jbc.M110.177618
↑ Noda NN, Kumeta H, Nakatogawa H, Satoo K, Adachi W, Ishii J, Fujioka Y, Ohsumi Y, Inagaki F. Structural basis of target recognition by Atg8/LC3 during selective autophagy. Genes Cells. 2008 Oct 22. PMID:19021777 doi:GTC1238
↑ Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F. Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34. J Biol Chem. 2010 Sep 24;285(39):30026-33. Epub 2010 Jul 21. PMID:20659891 doi:http://dx.doi.org/10.1074/jbc.M110.143545
↑ Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F. Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34. J Biol Chem. 2010 Sep 24;285(39):30026-33. Epub 2010 Jul 21. PMID:20659891 doi:http://dx.doi.org/10.1074/jbc.M110.143545

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/2kzb"

@@ Line 1: / Line 1: @@
 ==Solution structure of alpha-mannosidase binding domain of Atg19==
-<StructureSection load='2kzb' size='340' side='right' caption='[[2kzb]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2kzb' size='340' side='right'caption='[[2kzb]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2kzb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KZB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KZB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2kzb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KZB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KZB FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATG19, CVT19, YOL082W, YOL01, O0980 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2kzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kzb OCA], [http://pdbe.org/2kzb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kzb RCSB], [http://www.ebi.ac.uk/pdbsum/2kzb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kzb 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=2kzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kzb OCA], [https://pdbe.org/2kzb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kzb RCSB], [https://www.ebi.ac.uk/pdbsum/2kzb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kzb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ATG19_YEAST ATG19_YEAST]] Cargo-receptor protein involved in the cytoplasm to vacuole transport (Cvt) and in autophagy. Recognizes cargo proteins, such as APE4, LAP3, LAP4 and AMS1 and delivers them to the pre-autophagosomal structure for eventual engulfment by the autophagosome and targeting to the vacuole. Involved in the organization of the preautophagosomal structure (PAS). ATG19 association with cargo protein is required to localize ATG11 to the PAS. Also involved in endoplasmic reticulum-specific autophagic process, in selective removal of ER-associated degradation (ERAD) substrates, and is essential for the survival of cells subjected to severe ER stress. Plays also a role in regulation of filamentous growth.<ref>PMID:11382752</ref> <ref>PMID:11430817</ref> <ref>PMID:12479807</ref> <ref>PMID:12479808</ref> <ref>PMID:15138258</ref> <ref>PMID:15801807</ref> <ref>PMID:16186126</ref> <ref>PMID:15659643</ref> <ref>PMID:17132049</ref> <ref>PMID:17700056</ref> <ref>PMID:17192412</ref> <ref>PMID:17238920</ref> <ref>PMID:19061865</ref> <ref>PMID:21228276</ref> <ref>PMID:19021777</ref> <ref>PMID:20659891</ref>
+[https://www.uniprot.org/uniprot/ATG19_YEAST ATG19_YEAST] Cargo-receptor protein involved in the cytoplasm to vacuole transport (Cvt) and in autophagy. Recognizes cargo proteins, such as APE4, LAP3, LAP4 and AMS1 and delivers them to the pre-autophagosomal structure for eventual engulfment by the autophagosome and targeting to the vacuole. Involved in the organization of the preautophagosomal structure (PAS). ATG19 association with cargo protein is required to localize ATG11 to the PAS. Also involved in endoplasmic reticulum-specific autophagic process, in selective removal of ER-associated degradation (ERAD) substrates, and is essential for the survival of cells subjected to severe ER stress. Plays also a role in regulation of filamentous growth.<ref>PMID:11382752</ref> <ref>PMID:11430817</ref> <ref>PMID:12479807</ref> <ref>PMID:12479808</ref> <ref>PMID:15138258</ref> <ref>PMID:15801807</ref> <ref>PMID:16186126</ref> <ref>PMID:15659643</ref> <ref>PMID:17132049</ref> <ref>PMID:17700056</ref> <ref>PMID:17192412</ref> <ref>PMID:17238920</ref> <ref>PMID:19061865</ref> <ref>PMID:21228276</ref> <ref>PMID:19021777</ref> <ref>PMID:20659891</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 2kzb" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Autophagy-related protein 3D structures|Autophagy-related protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Inagaki, F]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Kumeta, H]]
+[[Category: Inagaki F]]
-[[Category: Noda, N]]
+[[Category: Kumeta H]]
-[[Category: Ohsumi, Y]]
+[[Category: Noda N]]
-[[Category: Suzuki, K]]
+[[Category: Ohsumi Y]]
-[[Category: Watanabe, Y]]
+[[Category: Suzuki K]]
-[[Category: Alpha-mannosidase]]
+[[Category: Watanabe Y]]
-[[Category: Atg19]]
-[[Category: Protein transport]]
-[[Category: Selective autophagy]]

2kzb

From Proteopedia

Current revision

Solution structure of alpha-mannosidase binding domain of Atg19

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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