8jtk: Difference between revisions

Latest revision as of 19:55, 29 May 2024

Structure of AYWB phytoplasma SAP05 recognizing AtRpn10

Structural highlights

8jtk is a 2 chain structure with sequence from Arabidopsis thaliana and Aster yellows witches'-broom phytoplasma AYWB. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.57Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSMD4_ARATH Plays a role in maintaining the structural integrity of the 19S regulatory particle (RP), subcomplex of the 26S proteasome. Plays a major role in both the direct and indirect recognition of ubiquitinated substrates of ubiquitin/26S proteasome-mediated proteolysis (UPP). Binds and presumably selects ubiquitin-conjugates for destruction. Prefers multiubiquitin chains rather than single ubiquitins, with a binding affinity for 'Lys-48'-linked ubiquitin chains. Acts as a potential docking subunit for both ubiquitin receptors RAD23s and DSK2s. Plays a role in the growth and development via the proteasome-dependent degradation of the ABA-signaling protein ABI5/DPBF1. Plays an important role for balancing cell expansion with cell proliferation rates during shoot development.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

References

↑ Smalle J, Kurepa J, Yang P, Emborg TJ, Babiychuk E, Kushnir S, Vierstra RD. The pleiotropic role of the 26S proteasome subunit RPN10 in Arabidopsis growth and development supports a substrate-specific function in abscisic acid signaling. Plant Cell. 2003 Apr;15(4):965-80. PMID:12671091 doi:10.1105/tpc.009217
↑ Kurepa J, Toh-E A, Smalle JA. 26S proteasome regulatory particle mutants have increased oxidative stress tolerance. Plant J. 2008 Jan;53(1):102-14. PMID:17971041 doi:10.1111/j.1365-313X.2007.03322.x
↑ Kurepa J, Wang S, Li Y, Zaitlin D, Pierce AJ, Smalle JA. Loss of 26S proteasome function leads to increased cell size and decreased cell number in Arabidopsis shoot organs. Plant Physiol. 2009 May;150(1):178-89. PMID:19321709 doi:10.1104/pp.109.135970
↑ Fatimababy AS, Lin YL, Usharani R, Radjacommare R, Wang HT, Tsai HL, Lee Y, Fu H. Cross-species divergence of the major recognition pathways of ubiquitylated substrates for ubiquitin/26S proteasome-mediated proteolysis. FEBS J. 2010 Feb;277(3):796-816. PMID:20059542 doi:10.1111/j.1742-4658.2009.07531.x
↑ Lin YL, Sung SC, Tsai HL, Yu TT, Radjacommare R, Usharani R, Fatimababy AS, Lin HY, Wang YY, Fu H. The defective proteasome but not substrate recognition function is responsible for the null phenotypes of the Arabidopsis proteasome subunit RPN10. Plant Cell. 2011 Jul;23(7):2754-73. PMID:21764993 doi:10.1105/tpc.111.086702
↑ Lin YL, Fu H. In vivo relevance of substrate recognition function of major Arabidopsis ubiquitin receptors. Plant Signal Behav. 2012 Jul;7(7):722-7. PMID:22751321 doi:10.4161/psb.20360
↑ Deveraux Q, van Nocker S, Mahaffey D, Vierstra R, Rechsteiner M. Inhibition of ubiquitin-mediated proteolysis by the Arabidopsis 26 S protease subunit S5a. J Biol Chem. 1995 Dec 15;270(50):29660-3. PMID:8530351 doi:10.1074/jbc.270.50.29660
↑ van Nocker S, Deveraux Q, Rechsteiner M, Vierstra RD. Arabidopsis MBP1 gene encodes a conserved ubiquitin recognition component of the 26S proteasome. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):856-60. PMID:8570648 doi:10.1073/pnas.93.2.856
↑ Fu H, Sadis S, Rubin DM, Glickman M, van Nocker S, Finley D, Vierstra RD. Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1. J Biol Chem. 1998 Jan 23;273(4):1970-81. PMID:9442033 doi:10.1074/jbc.273.4.1970
↑ Glickman MH, Rubin DM, Coux O, Wefes I, Pfeifer G, Cjeka Z, Baumeister W, Fried VA, Finley D. A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell. 1998 Sep 4;94(5):615-23. PMID:9741626 doi:10.1016/s0092-8674(00)81603-7

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Smalle J, Kurepa J, Yang P, Emborg TJ, Babiychuk E, Kushnir S, Vierstra RD. The pleiotropic role of the 26S proteasome subunit RPN10 in Arabidopsis growth and development supports a substrate-specific function in abscisic acid signaling. Plant Cell. 2003 Apr;15(4):965-80. PMID:12671091 doi:10.1105/tpc.009217

[2] Kurepa J, Toh-E A, Smalle JA. 26S proteasome regulatory particle mutants have increased oxidative stress tolerance. Plant J. 2008 Jan;53(1):102-14. PMID:17971041 doi:10.1111/j.1365-313X.2007.03322.x

[3] Kurepa J, Wang S, Li Y, Zaitlin D, Pierce AJ, Smalle JA. Loss of 26S proteasome function leads to increased cell size and decreased cell number in Arabidopsis shoot organs. Plant Physiol. 2009 May;150(1):178-89. PMID:19321709 doi:10.1104/pp.109.135970

[4] Fatimababy AS, Lin YL, Usharani R, Radjacommare R, Wang HT, Tsai HL, Lee Y, Fu H. Cross-species divergence of the major recognition pathways of ubiquitylated substrates for ubiquitin/26S proteasome-mediated proteolysis. FEBS J. 2010 Feb;277(3):796-816. PMID:20059542 doi:10.1111/j.1742-4658.2009.07531.x

[5] Lin YL, Sung SC, Tsai HL, Yu TT, Radjacommare R, Usharani R, Fatimababy AS, Lin HY, Wang YY, Fu H. The defective proteasome but not substrate recognition function is responsible for the null phenotypes of the Arabidopsis proteasome subunit RPN10. Plant Cell. 2011 Jul;23(7):2754-73. PMID:21764993 doi:10.1105/tpc.111.086702

[6] Lin YL, Fu H. In vivo relevance of substrate recognition function of major Arabidopsis ubiquitin receptors. Plant Signal Behav. 2012 Jul;7(7):722-7. PMID:22751321 doi:10.4161/psb.20360

[7] Deveraux Q, van Nocker S, Mahaffey D, Vierstra R, Rechsteiner M. Inhibition of ubiquitin-mediated proteolysis by the Arabidopsis 26 S protease subunit S5a. J Biol Chem. 1995 Dec 15;270(50):29660-3. PMID:8530351 doi:10.1074/jbc.270.50.29660

[8] van Nocker S, Deveraux Q, Rechsteiner M, Vierstra RD. Arabidopsis MBP1 gene encodes a conserved ubiquitin recognition component of the 26S proteasome. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):856-60. PMID:8570648 doi:10.1073/pnas.93.2.856

[9] Fu H, Sadis S, Rubin DM, Glickman M, van Nocker S, Finley D, Vierstra RD. Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1. J Biol Chem. 1998 Jan 23;273(4):1970-81. PMID:9442033 doi:10.1074/jbc.273.4.1970

[10] Glickman MH, Rubin DM, Coux O, Wefes I, Pfeifer G, Cjeka Z, Baumeister W, Fried VA, Finley D. A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell. 1998 Sep 4;94(5):615-23. PMID:9741626 doi:10.1016/s0092-8674(00)81603-7

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8jtk is ON HOLD
+==Structure of AYWB phytoplasma SAP05 recognizing AtRpn10==
+<StructureSection load='8jtk' size='340' side='right'caption='[[8jtk]], [[Resolution|resolution]] 1.57&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8jtk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Aster_yellows_witches'-broom_phytoplasma_AYWB Aster yellows witches'-broom phytoplasma AYWB]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8JTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JTK 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]] 1.57&#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=8jtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8jtk OCA], [https://pdbe.org/8jtk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8jtk RCSB], [https://www.ebi.ac.uk/pdbsum/8jtk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8jtk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSMD4_ARATH PSMD4_ARATH] Plays a role in maintaining the structural integrity of the 19S regulatory particle (RP), subcomplex of the 26S proteasome. Plays a major role in both the direct and indirect recognition of ubiquitinated substrates of ubiquitin/26S proteasome-mediated proteolysis (UPP). Binds and presumably selects ubiquitin-conjugates for destruction. Prefers multiubiquitin chains rather than single ubiquitins, with a binding affinity for 'Lys-48'-linked ubiquitin chains. Acts as a potential docking subunit for both ubiquitin receptors RAD23s and DSK2s. Plays a role in the growth and development via the proteasome-dependent degradation of the ABA-signaling protein ABI5/DPBF1. Plays an important role for balancing cell expansion with cell proliferation rates during shoot development.<ref>PMID:12671091</ref> <ref>PMID:17971041</ref> <ref>PMID:19321709</ref> <ref>PMID:20059542</ref> <ref>PMID:21764993</ref> <ref>PMID:22751321</ref> <ref>PMID:8530351</ref> <ref>PMID:8570648</ref> <ref>PMID:9442033</ref> <ref>PMID:9741626</ref>
-Authors: Du, Y.X., Zhang, L.Y., Zheng, Q.Y.
+==See Also==
+*[[Proteasome 3D structures|Proteasome 3D structures]]
-Description: Structure of AYWB phytoplasma SAP05_vWA recognizing AtRpn10
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
-[[Category: Zhang, L.Y]]
+__TOC__
-[[Category: Du, Y.X]]
+</StructureSection>
-[[Category: Zheng, Q.Y]]
+[[Category: Arabidopsis thaliana]]
+[[Category: Aster yellows witches'-broom phytoplasma AYWB]]
+[[Category: Large Structures]]
+[[Category: Du YX]]
+[[Category: Zhang LY]]
+[[Category: Zheng QY]]

8jtk: Difference between revisions

Latest revision as of 19:55, 29 May 2024

Structure of AYWB phytoplasma SAP05 recognizing AtRpn10

Structural highlights

Function

See Also

References

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