3vp7: Difference between revisions

Latest revision as of 14:13, 18 October 2023

Crystal structure of the beta-alpha repeated, autophagy-specific (BARA) domain of Vps30/Atg6

Structural highlights

3vp7 is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BECN1_YEAST Required for cytoplasm to vacuole transport (Cvt), autophagy, nucleophagy, and mitophagy, as a part of the autophagy-specific VPS34 PI3-kinase complex I. This complex is essential to recruit the ATG8-phosphatidylinositol conjugate and the ATG12-ATG5 conjugate to the pre-autophagosomal structure. Also involved in endosome-to-Golgi retrograde transport as part of the VPS34 PI3-kinase complex II. This second complex is required for the endosome-to-Golgi retrieval of PEP1 and KEX2, and the recruitment of VPS5 and VPS7, two components of the retromer complex, to endosomal membranes (probably through the synthesis of a specific pool of phosphatidylinositol 3-phosphate recruiting the retromer to the endosomes). Plays also a role in regulation of filamentous growth.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14]

References

↑ Kihara A, Noda T, Ishihara N, Ohsumi Y. Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J Cell Biol. 2001 Feb 5;152(3):519-30. PMID:11157979
↑ 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
↑ Burda P, Padilla SM, Sarkar S, Emr SD. Retromer function in endosome-to-Golgi retrograde transport is regulated by the yeast Vps34 PtdIns 3-kinase. J Cell Sci. 2002 Oct 15;115(Pt 20):3889-900. PMID:12244127
↑ Kruse KB, Brodsky JL, McCracken AA. Characterization of an ERAD gene as VPS30/ATG6 reveals two alternative and functionally distinct protein quality control pathways: one for soluble Z variant of human alpha-1 proteinase inhibitor (A1PiZ) and another for aggregates of A1PiZ. Mol Biol Cell. 2006 Jan;17(1):203-12. Epub 2005 Nov 2. PMID:16267277 doi:https://dx.doi.org/10.1091/mbc.E04-09-0779
↑ Zhang Y, Qi H, Taylor R, Xu W, Liu LF, Jin S. The role of autophagy in mitochondria maintenance: characterization of mitochondrial functions in autophagy-deficient S. cerevisiae strains. Autophagy. 2007 Jul-Aug;3(4):337-46. Epub 2007 Jul 9. PMID:17404498
↑ 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
↑ Hirayama H, Fujita M, Yoko-o T, Jigami Y. O-mannosylation is required for degradation of the endoplasmic reticulum-associated degradation substrate Gas1*p via the ubiquitin/proteasome pathway in Saccharomyces cerevisiae. J Biochem. 2008 Apr;143(4):555-67. doi: 10.1093/jb/mvm249. Epub 2008 Jan 7. PMID:18182384 doi:https://dx.doi.org/10.1093/jb/mvm249
↑ Krick R, Muehe Y, Prick T, Bremer S, Schlotterhose P, Eskelinen EL, Millen J, Goldfarb DS, Thumm M. Piecemeal microautophagy of the nucleus requires the core macroautophagy genes. Mol Biol Cell. 2008 Oct;19(10):4492-505. doi: 10.1091/mbc.E08-04-0363. Epub 2008 , Aug 13. PMID:18701704 doi:https://dx.doi.org/10.1091/mbc.E08-04-0363
↑ Fu L, Sztul E. ER-associated complexes (ERACs) containing aggregated cystic fibrosis transmembrane conductance regulator (CFTR) are degraded by autophagy. Eur J Cell Biol. 2009 Apr;88(4):215-26. doi: 10.1016/j.ejcb.2008.11.003. Epub, 2009 Jan 7. PMID:19131141 doi:https://dx.doi.org/10.1016/j.ejcb.2008.11.003
↑ Noda NN, Kobayashi T, Adachi W, Fujioka Y, Ohsumi Y, Inagaki F. Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy. J Biol Chem. 2012 May 11;287(20):16256-66. doi: 10.1074/jbc.M112.348250. Epub, 2012 Mar 21. PMID:22437838 doi:https://dx.doi.org/10.1074/jbc.M112.348250
↑ Fogel AI, Dlouhy BJ, Wang C, Ryu SW, Neutzner A, Hasson SA, Sideris DP, Abeliovich H, Youle RJ. Role of membrane association and Atg14-dependent phosphorylation in beclin-1-mediated autophagy. Mol Cell Biol. 2013 Sep;33(18):3675-88. doi: 10.1128/MCB.00079-13. Epub 2013 Jul , 22. PMID:23878393 doi:https://dx.doi.org/10.1128/MCB.00079-13
↑ 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
↑ Seaman MN, Marcusson EG, Cereghino JL, Emr SD. Endosome to Golgi retrieval of the vacuolar protein sorting receptor, Vps10p, requires the function of the VPS29, VPS30, and VPS35 gene products. J Cell Biol. 1997 Apr 7;137(1):79-92. PMID:9105038
↑ Kametaka S, Okano T, Ohsumi M, Ohsumi Y. Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae. J Biol Chem. 1998 Aug 28;273(35):22284-91. PMID:9712845

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OCA

[1] Kihara A, Noda T, Ishihara N, Ohsumi Y. Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J Cell Biol. 2001 Feb 5;152(3):519-30. PMID:11157979

[2] 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

[3] Burda P, Padilla SM, Sarkar S, Emr SD. Retromer function in endosome-to-Golgi retrograde transport is regulated by the yeast Vps34 PtdIns 3-kinase. J Cell Sci. 2002 Oct 15;115(Pt 20):3889-900. PMID:12244127

[4] Kruse KB, Brodsky JL, McCracken AA. Characterization of an ERAD gene as VPS30/ATG6 reveals two alternative and functionally distinct protein quality control pathways: one for soluble Z variant of human alpha-1 proteinase inhibitor (A1PiZ) and another for aggregates of A1PiZ. Mol Biol Cell. 2006 Jan;17(1):203-12. Epub 2005 Nov 2. PMID:16267277 doi:https://dx.doi.org/10.1091/mbc.E04-09-0779

[5] Zhang Y, Qi H, Taylor R, Xu W, Liu LF, Jin S. The role of autophagy in mitochondria maintenance: characterization of mitochondrial functions in autophagy-deficient S. cerevisiae strains. Autophagy. 2007 Jul-Aug;3(4):337-46. Epub 2007 Jul 9. PMID:17404498

[6] 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

[7] Hirayama H, Fujita M, Yoko-o T, Jigami Y. O-mannosylation is required for degradation of the endoplasmic reticulum-associated degradation substrate Gas1*p via the ubiquitin/proteasome pathway in Saccharomyces cerevisiae. J Biochem. 2008 Apr;143(4):555-67. doi: 10.1093/jb/mvm249. Epub 2008 Jan 7. PMID:18182384 doi:https://dx.doi.org/10.1093/jb/mvm249

[8] Krick R, Muehe Y, Prick T, Bremer S, Schlotterhose P, Eskelinen EL, Millen J, Goldfarb DS, Thumm M. Piecemeal microautophagy of the nucleus requires the core macroautophagy genes. Mol Biol Cell. 2008 Oct;19(10):4492-505. doi: 10.1091/mbc.E08-04-0363. Epub 2008 , Aug 13. PMID:18701704 doi:https://dx.doi.org/10.1091/mbc.E08-04-0363

[9] Fu L, Sztul E. ER-associated complexes (ERACs) containing aggregated cystic fibrosis transmembrane conductance regulator (CFTR) are degraded by autophagy. Eur J Cell Biol. 2009 Apr;88(4):215-26. doi: 10.1016/j.ejcb.2008.11.003. Epub, 2009 Jan 7. PMID:19131141 doi:https://dx.doi.org/10.1016/j.ejcb.2008.11.003

[10] Noda NN, Kobayashi T, Adachi W, Fujioka Y, Ohsumi Y, Inagaki F. Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy. J Biol Chem. 2012 May 11;287(20):16256-66. doi: 10.1074/jbc.M112.348250. Epub, 2012 Mar 21. PMID:22437838 doi:https://dx.doi.org/10.1074/jbc.M112.348250

[11] Fogel AI, Dlouhy BJ, Wang C, Ryu SW, Neutzner A, Hasson SA, Sideris DP, Abeliovich H, Youle RJ. Role of membrane association and Atg14-dependent phosphorylation in beclin-1-mediated autophagy. Mol Cell Biol. 2013 Sep;33(18):3675-88. doi: 10.1128/MCB.00079-13. Epub 2013 Jul , 22. PMID:23878393 doi:https://dx.doi.org/10.1128/MCB.00079-13

[12] 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

[13] Seaman MN, Marcusson EG, Cereghino JL, Emr SD. Endosome to Golgi retrieval of the vacuolar protein sorting receptor, Vps10p, requires the function of the VPS29, VPS30, and VPS35 gene products. J Cell Biol. 1997 Apr 7;137(1):79-92. PMID:9105038

[14] Kametaka S, Okano T, Ohsumi M, Ohsumi Y. Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae. J Biol Chem. 1998 Aug 28;273(35):22284-91. PMID:9712845

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 3vp7 is ON HOLD
+==Crystal structure of the beta-alpha repeated, autophagy-specific (BARA) domain of Vps30/Atg6==
+<StructureSection load='3vp7' size='340' side='right'caption='[[3vp7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3vp7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VP7 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=3vp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vp7 OCA], [https://pdbe.org/3vp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vp7 RCSB], [https://www.ebi.ac.uk/pdbsum/3vp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vp7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BECN1_YEAST BECN1_YEAST] Required for cytoplasm to vacuole transport (Cvt), autophagy, nucleophagy, and mitophagy, as a part of the autophagy-specific VPS34 PI3-kinase complex I. This complex is essential to recruit the ATG8-phosphatidylinositol conjugate and the ATG12-ATG5 conjugate to the pre-autophagosomal structure. Also involved in endosome-to-Golgi retrograde transport as part of the VPS34 PI3-kinase complex II. This second complex is required for the endosome-to-Golgi retrieval of PEP1 and KEX2, and the recruitment of VPS5 and VPS7, two components of the retromer complex, to endosomal membranes (probably through the synthesis of a specific pool of phosphatidylinositol 3-phosphate recruiting the retromer to the endosomes). Plays also a role in regulation of filamentous growth.<ref>PMID:11157979</ref> <ref>PMID:11689437</ref> <ref>PMID:12244127</ref> <ref>PMID:16267277</ref> <ref>PMID:17404498</ref> <ref>PMID:17700056</ref> <ref>PMID:18182384</ref> <ref>PMID:18701704</ref> <ref>PMID:19131141</ref> <ref>PMID:22437838</ref> <ref>PMID:23878393</ref> <ref>PMID:8224160</ref> <ref>PMID:9105038</ref> <ref>PMID:9712845</ref>
-Authors: Noda, N.N., Kobayashi, T., Adachi, W., Fujioka, Y., Ohsumi, Y., Inagaki, F.
+==See Also==
+*[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]]
-Description: Crystal structure of the beta-alpha repeated, autophagy-specific (BARA) domain of Vps30/Atg6
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Adachi W]]
+[[Category: Fujioka Y]]
+[[Category: Inagaki F]]
+[[Category: Kobayashi T]]
+[[Category: Noda NN]]
+[[Category: Ohsumi Y]]

3vp7: Difference between revisions

Latest revision as of 14:13, 18 October 2023

Crystal structure of the beta-alpha repeated, autophagy-specific (BARA) domain of Vps30/Atg6

Structural highlights

Function

See Also

References

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