5jm9

From Proteopedia

(Difference between revisions)

Current revision

Structure of S. cerevesiae mApe1 dodecamer

5jm9, resolution 24.00Å

Structural highlights

5jm9 is a 1 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:	Electron Microscopy, Resolution 24Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMPL_YEAST Resident vacuolar enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins. Also acts as the major cargo protein of the cytoplasm-to-vacuole targeting (Cvt) pathway. The precursor form of aminopeptidase 1 (prApe1) assembles into dodecamers and the propeptide mediates the aggregation of dodecamers into higher multimers. The multimers are then recognized via the propeptide by their receptor ATG19, and ATG19 further interacts with ATG11, which tethers the APE1-ATG19 complex to the pre-autophagosomal structure (PAS). The cargo-receptor complex (also Cvt complex) is selectively enwrapped by a double-membrane structure termed the Cvt vesicle under vegetative growth conditions and by a similar but larger double-membrane structure termed the autophagosome under nitrogen starvation conditions. The Cvt vesicle or the autophagosome fuses with the vacuolar membrane and release its content in the vacuolar lumen. In the vacuole, prApe1 is processed into mature aminopeptidase 1 (mApe1).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

Selective autophagy is the mechanism by which large cargos are specifically sequestered for degradation. The structural details of cargo and receptor assembly giving rise to autophagic vesicles remain to be elucidated. We utilize the yeast cytoplasm-to-vacuole targeting (Cvt) pathway, a prototype of selective autophagy, together with a multi-scale analysis approach to study the molecular structure of Cvt vesicles. We report the oligomeric nature of the major Cvt cargo Ape1 with a combined 2.8 A X-ray and negative stain EM structure, as well as the secondary cargo Ams1 with a 6.3 A cryo-EM structure. We show that the major dodecameric cargo prApe1 exhibits a tendency to form higher-order chain structures that are broken upon interaction with the receptor Atg19 in vitro The stoichiometry of these cargo-receptor complexes is key to maintaining the size of the Cvt aggregate in vivo Using correlative light and electron microscopy, we further visualize key stages of Cvt vesicle biogenesis. Our findings suggest that Atg19 interaction limits Ape1 aggregate size while serving as a vehicle for vacuolar delivery of tetrameric Ams1.

Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle.,Bertipaglia C, Schneider S, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJ, Ravichandran AC, Wilmanns M, Kaksonen M, Briggs JA, Sachse C EMBO Rep. 2016 Jun 6. pii: e201541960. PMID:27266708^[9]

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
↑ 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
↑ Morales Quinones M, Winston JT, Stromhaug PE. Propeptide of aminopeptidase 1 protein mediates aggregation and vesicle formation in cytoplasm-to-vacuole targeting pathway. J Biol Chem. 2012 Mar 23;287(13):10121-33. doi: 10.1074/jbc.M111.311696. Epub, 2011 Nov 28. PMID:22123825 doi:http://dx.doi.org/10.1074/jbc.M111.311696
↑ Frey J, Rohm KH. Subcellular localization and levels of aminopeptidases and dipeptidase in Saccharomyces cerevisiae. Biochim Biophys Acta. 1978 Nov 10;527(1):31-41. PMID:363165
↑ Scott SV, Hefner-Gravink A, Morano KA, Noda T, Ohsumi Y, Klionsky DJ. Cytoplasm-to-vacuole targeting and autophagy employ the same machinery to deliver proteins to the yeast vacuole. Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12304-8. PMID:8901576
↑ Scott SV, Baba M, Ohsumi Y, Klionsky DJ. Aminopeptidase I is targeted to the vacuole by a nonclassical vesicular mechanism. J Cell Biol. 1997 Jul 14;138(1):37-44. PMID:9214379
↑ Baba M, Osumi M, Scott SV, Klionsky DJ, Ohsumi Y. Two distinct pathways for targeting proteins from the cytoplasm to the vacuole/lysosome. J Cell Biol. 1997 Dec 29;139(7):1687-95. PMID:9412464
↑ Bertipaglia C, Schneider S, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJ, Ravichandran AC, Wilmanns M, Kaksonen M, Briggs JA, Sachse C. Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. EMBO Rep. 2016 Jun 6. pii: e201541960. PMID:27266708 doi:http://dx.doi.org/10.15252/embr.201541960

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/5jm9"

Categories: Large Structures | Saccharomyces cerevisiae | Bertipaglia C | Sachse C

@@ Line 1: / Line 1: @@
 ==Structure of S. cerevesiae mApe1 dodecamer==
-<StructureSection load='5jm9' size='340' side='right' caption='[[5jm9]], [[Resolution|resolution]] 24.00&Aring;' scene=''>
+<SX load='5jm9' size='340' side='right' viewer='molstar' caption='[[5jm9]], [[Resolution|resolution]] 24.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jm9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JM9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jm9]] is a 1 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=5JM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JM9 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE1, API, LAP4, YSC1, YKL103C, YKL455 ([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">Electron Microscopy, [[Resolution|Resolution]] 24&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminopeptidase_I Aminopeptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.22 3.4.11.22] </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=5jm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jm9 OCA], [https://pdbe.org/5jm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jm9 RCSB], [https://www.ebi.ac.uk/pdbsum/5jm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jm9 ProSAT]</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=5jm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jm9 OCA], [http://pdbe.org/5jm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jm9 RCSB], [http://www.ebi.ac.uk/pdbsum/5jm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jm9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AMPL_YEAST AMPL_YEAST]] Resident vacuolar enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins. Also acts as the major cargo protein of the cytoplasm-to-vacuole targeting (Cvt) pathway. The precursor form of aminopeptidase 1 (prApe1) assembles into dodecamers and the propeptide mediates the aggregation of dodecamers into higher multimers. The multimers are then recognized via the propeptide by their receptor ATG19, and ATG19 further interacts with ATG11, which tethers the APE1-ATG19 complex to the pre-autophagosomal structure (PAS). The cargo-receptor complex (also Cvt complex) is selectively enwrapped by a double-membrane structure termed the Cvt vesicle under vegetative growth conditions and by a similar but larger double-membrane structure termed the autophagosome under nitrogen starvation conditions. The Cvt vesicle or the autophagosome fuses with the vacuolar membrane and release its content in the vacuolar lumen. In the vacuole, prApe1 is processed into mature aminopeptidase 1 (mApe1).<ref>PMID:11382752</ref> <ref>PMID:11430817</ref> <ref>PMID:15138258</ref> <ref>PMID:22123825</ref> <ref>PMID:363165</ref> <ref>PMID:8901576</ref> <ref>PMID:9214379</ref> <ref>PMID:9412464</ref>
+[https://www.uniprot.org/uniprot/AMPL_YEAST AMPL_YEAST] Resident vacuolar enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins. Also acts as the major cargo protein of the cytoplasm-to-vacuole targeting (Cvt) pathway. The precursor form of aminopeptidase 1 (prApe1) assembles into dodecamers and the propeptide mediates the aggregation of dodecamers into higher multimers. The multimers are then recognized via the propeptide by their receptor ATG19, and ATG19 further interacts with ATG11, which tethers the APE1-ATG19 complex to the pre-autophagosomal structure (PAS). The cargo-receptor complex (also Cvt complex) is selectively enwrapped by a double-membrane structure termed the Cvt vesicle under vegetative growth conditions and by a similar but larger double-membrane structure termed the autophagosome under nitrogen starvation conditions. The Cvt vesicle or the autophagosome fuses with the vacuolar membrane and release its content in the vacuolar lumen. In the vacuole, prApe1 is processed into mature aminopeptidase 1 (mApe1).<ref>PMID:11382752</ref> <ref>PMID:11430817</ref> <ref>PMID:15138258</ref> <ref>PMID:22123825</ref> <ref>PMID:363165</ref> <ref>PMID:8901576</ref> <ref>PMID:9214379</ref> <ref>PMID:9412464</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 18: @@
 </div>
 <div class="pdbe-citations 5jm9" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Aminopeptidase I]]
+[[Category: Large Structures]]
-[[Category: Atcc 18824]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Bertipaglia, C]]
+[[Category: Bertipaglia C]]
-[[Category: Sachse, C]]
+[[Category: Sachse C]]
-[[Category: Aminopeptidase]]
-[[Category: Cvt]]
-[[Category: Dodecamer]]
-[[Category: Hydrolase]]
-[[Category: Vacuole]]

5jm9

From Proteopedia

Current revision

Structure of S. cerevesiae mApe1 dodecamer

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox