7kpx: Difference between revisions

Latest revision as of 14:57, 6 March 2024

Structure of the yeast CKM

Structural highlights

7kpx is a 4 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:	Electron Microscopy, Resolution 4.4Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SSN3_YEAST Component of the SRB8-11 complex. The SRB8-11 complex is a regulatory module of the Mediator complex which is itself involved in regulation of basal and activated RNA polymerase II-dependent transcription. The SRB8-11 complex may be involved in the transcriptional repression of a subset of genes regulated by Mediator. It may inhibit the association of the Mediator complex with RNA polymerase II to form the holoenzyme complex. The SRB8-11 complex phosphorylates the C-terminal domain (CTD) of the largest subunit of RNA polymerase II RPB1 at serines 2 and 5. The SSN3/SRB10 and SSN8/SRB11 kinase-cyclin pair may also positively and negatively regulate numerous transcriptional activators in response to changes in nutritional and physiological conditions. Phosphorylates GCN4, promoting its ubiquitin-mediated degradation, and MSN2, promoting its nuclear exclusion. Phosphorylates STE12, thereby promoting its degradation and inhibition of filamentous growth. Phosphorylates GAL4, and this phosphorylation is required for efficient galactose-inducible transcription. Also phosphorylates BDF1 and the TAF2 subunit of the TFIID complex.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17]

References

↑ Hirst M, Kobor MS, Kuriakose N, Greenblatt J, Sadowski I. GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. Mol Cell. 1999 May;3(5):673-8. PMID:10360183 doi:10.1016/s1097-2765(00)80360-3
↑ Zaman Z, Ansari AZ, Koh SS, Young R, Ptashne M. Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2550-4. PMID:11226276 doi:10.1073/pnas.041611198
↑ Chi Y, Huddleston MJ, Zhang X, Young RA, Annan RS, Carr SA, Deshaies RJ. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 2001 May 1;15(9):1078-92. PMID:11331604 doi:10.1101/gad.867501
↑ Kang JS, Kim SH, Hwang MS, Han SJ, Lee YC, Kim YJ. The structural and functional organization of the yeast mediator complex. J Biol Chem. 2001 Nov 9;276(45):42003-10. Epub 2001 Sep 12. PMID:11555651 doi:https://dx.doi.org/10.1074/jbc.M105961200
↑ Borggrefe T, Davis R, Erdjument-Bromage H, Tempst P, Kornberg RD. A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J Biol Chem. 2002 Nov 15;277(46):44202-7. PMID:12200444 doi:10.1074/jbc.M207195200
↑ Nelson C, Goto S, Lund K, Hung W, Sadowski I. Srb10/Cdk8 regulates yeast filamentous growth by phosphorylating the transcription factor Ste12. Nature. 2003 Jan 9;421(6919):187-90. PMID:12520306 doi:10.1038/nature01243
↑ Liu Y, Kung C, Fishburn J, Ansari AZ, Shokat KM, Hahn S. Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol Cell Biol. 2004 Feb;24(4):1721-35. PMID:14749387 doi:10.1128/MCB.24.4.1721-1735.2004
↑ Hallberg M, Polozkov GV, Hu GZ, Beve J, Gustafsson CM, Ronne H, Björklund S. Site-specific Srb10-dependent phosphorylation of the yeast Mediator subunit Med2 regulates gene expression from the 2-microm plasmid. Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3370-5. PMID:14988503 doi:10.1073/pnas.0400221101
↑ Green SR, Johnson AD. Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae. Mol Biol Cell. 2004 Sep;15(9):4191-202. PMID:15240822 doi:10.1091/mbc.e04-05-0412
↑ Larschan E, Winston F. The Saccharomyces cerevisiae Srb8-Srb11 complex functions with the SAGA complex during Gal4-activated transcription. Mol Cell Biol. 2005 Jan;25(1):114-23. PMID:15601835 doi:10.1128/MCB.25.1.114-123.2005
↑ Ansari AZ, Ogirala A, Ptashne M. Transcriptional activating regions target attached substrates to a cyclin-dependent kinase. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2346-9. PMID:15687503 doi:10.1073/pnas.0409671102
↑ Nair D, Kim Y, Myers LC. Mediator and TFIIH govern carboxyl-terminal domain-dependent transcription in yeast extracts. J Biol Chem. 2005 Oct 7;280(40):33739-48. Epub 2005 Aug 2. PMID:16076843 doi:https://dx.doi.org/M506067200
↑ van de Peppel J, Kettelarij N, van Bakel H, Kockelkorn TT, van Leenen D, Holstege FC. Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol Cell. 2005 Aug 19;19(4):511-22. PMID:16109375 doi:https://dx.doi.org/10.1016/j.molcel.2005.06.033
↑ Andrau JC, van de Pasch L, Lijnzaad P, Bijma T, Koerkamp MG, van de Peppel J, Werner M, Holstege FC. Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol Cell. 2006 Apr 21;22(2):179-92. PMID:16630888 doi:https://dx.doi.org/S1097-2765(06)00189-4
↑ Liao SM, Zhang J, Jeffery DA, Koleske AJ, Thompson CM, Chao DM, Viljoen M, van Vuuren HJ, Young RA. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature. 1995 Mar 9;374(6518):193-6. PMID:7877695 doi:10.1038/374193a0
↑ Hengartner CJ, Myer VE, Liao SM, Wilson CJ, Koh SS, Young RA. Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol Cell. 1998 Jul;2(1):43-53. PMID:9702190 doi:10.1016/s1097-2765(00)80112-4
↑ Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998 Nov 25;95(5):717-28. PMID:9845373

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hirst M, Kobor MS, Kuriakose N, Greenblatt J, Sadowski I. GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. Mol Cell. 1999 May;3(5):673-8. PMID:10360183 doi:10.1016/s1097-2765(00)80360-3

[2] Zaman Z, Ansari AZ, Koh SS, Young R, Ptashne M. Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2550-4. PMID:11226276 doi:10.1073/pnas.041611198

[3] Chi Y, Huddleston MJ, Zhang X, Young RA, Annan RS, Carr SA, Deshaies RJ. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 2001 May 1;15(9):1078-92. PMID:11331604 doi:10.1101/gad.867501

[4] Kang JS, Kim SH, Hwang MS, Han SJ, Lee YC, Kim YJ. The structural and functional organization of the yeast mediator complex. J Biol Chem. 2001 Nov 9;276(45):42003-10. Epub 2001 Sep 12. PMID:11555651 doi:https://dx.doi.org/10.1074/jbc.M105961200

[5] Borggrefe T, Davis R, Erdjument-Bromage H, Tempst P, Kornberg RD. A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J Biol Chem. 2002 Nov 15;277(46):44202-7. PMID:12200444 doi:10.1074/jbc.M207195200

[6] Nelson C, Goto S, Lund K, Hung W, Sadowski I. Srb10/Cdk8 regulates yeast filamentous growth by phosphorylating the transcription factor Ste12. Nature. 2003 Jan 9;421(6919):187-90. PMID:12520306 doi:10.1038/nature01243

[7] Liu Y, Kung C, Fishburn J, Ansari AZ, Shokat KM, Hahn S. Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol Cell Biol. 2004 Feb;24(4):1721-35. PMID:14749387 doi:10.1128/MCB.24.4.1721-1735.2004

[8] Hallberg M, Polozkov GV, Hu GZ, Beve J, Gustafsson CM, Ronne H, Björklund S. Site-specific Srb10-dependent phosphorylation of the yeast Mediator subunit Med2 regulates gene expression from the 2-microm plasmid. Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3370-5. PMID:14988503 doi:10.1073/pnas.0400221101

[9] Green SR, Johnson AD. Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae. Mol Biol Cell. 2004 Sep;15(9):4191-202. PMID:15240822 doi:10.1091/mbc.e04-05-0412

[10] Larschan E, Winston F. The Saccharomyces cerevisiae Srb8-Srb11 complex functions with the SAGA complex during Gal4-activated transcription. Mol Cell Biol. 2005 Jan;25(1):114-23. PMID:15601835 doi:10.1128/MCB.25.1.114-123.2005

[11] Ansari AZ, Ogirala A, Ptashne M. Transcriptional activating regions target attached substrates to a cyclin-dependent kinase. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2346-9. PMID:15687503 doi:10.1073/pnas.0409671102

[12] Nair D, Kim Y, Myers LC. Mediator and TFIIH govern carboxyl-terminal domain-dependent transcription in yeast extracts. J Biol Chem. 2005 Oct 7;280(40):33739-48. Epub 2005 Aug 2. PMID:16076843 doi:https://dx.doi.org/M506067200

[13] van de Peppel J, Kettelarij N, van Bakel H, Kockelkorn TT, van Leenen D, Holstege FC. Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol Cell. 2005 Aug 19;19(4):511-22. PMID:16109375 doi:https://dx.doi.org/10.1016/j.molcel.2005.06.033

[14] Andrau JC, van de Pasch L, Lijnzaad P, Bijma T, Koerkamp MG, van de Peppel J, Werner M, Holstege FC. Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol Cell. 2006 Apr 21;22(2):179-92. PMID:16630888 doi:https://dx.doi.org/S1097-2765(06)00189-4

[15] Liao SM, Zhang J, Jeffery DA, Koleske AJ, Thompson CM, Chao DM, Viljoen M, van Vuuren HJ, Young RA. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature. 1995 Mar 9;374(6518):193-6. PMID:7877695 doi:10.1038/374193a0

[16] Hengartner CJ, Myer VE, Liao SM, Wilson CJ, Koh SS, Young RA. Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol Cell. 1998 Jul;2(1):43-53. PMID:9702190 doi:10.1016/s1097-2765(00)80112-4

[17] Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998 Nov 25;95(5):717-28. PMID:9845373

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@@ Line 1: / Line 1: @@
-====
+==Structure of the yeast CKM==
-<StructureSection load='7kpx' size='340' side='right'caption='[[7kpx]]' scene=''>
+<StructureSection load='7kpx' size='340' side='right'caption='[[7kpx]], [[Resolution|resolution]] 4.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7kpx]] is a 4 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=7KPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KPX 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=7kpx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kpx OCA], [https://pdbe.org/7kpx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kpx RCSB], [https://www.ebi.ac.uk/pdbsum/7kpx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kpx ProSAT]</span></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]] 4.4&#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=7kpx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kpx OCA], [https://pdbe.org/7kpx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kpx RCSB], [https://www.ebi.ac.uk/pdbsum/7kpx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kpx ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SSN3_YEAST SSN3_YEAST] Component of the SRB8-11 complex. The SRB8-11 complex is a regulatory module of the Mediator complex which is itself involved in regulation of basal and activated RNA polymerase II-dependent transcription. The SRB8-11 complex may be involved in the transcriptional repression of a subset of genes regulated by Mediator. It may inhibit the association of the Mediator complex with RNA polymerase II to form the holoenzyme complex. The SRB8-11 complex phosphorylates the C-terminal domain (CTD) of the largest subunit of RNA polymerase II RPB1 at serines 2 and 5. The SSN3/SRB10 and SSN8/SRB11 kinase-cyclin pair may also positively and negatively regulate numerous transcriptional activators in response to changes in nutritional and physiological conditions. Phosphorylates GCN4, promoting its ubiquitin-mediated degradation, and MSN2, promoting its nuclear exclusion. Phosphorylates STE12, thereby promoting its degradation and inhibition of filamentous growth. Phosphorylates GAL4, and this phosphorylation is required for efficient galactose-inducible transcription. Also phosphorylates BDF1 and the TAF2 subunit of the TFIID complex.<ref>PMID:10360183</ref> <ref>PMID:11226276</ref> <ref>PMID:11331604</ref> <ref>PMID:11555651</ref> <ref>PMID:12200444</ref> <ref>PMID:12520306</ref> <ref>PMID:14749387</ref> <ref>PMID:14988503</ref> <ref>PMID:15240822</ref> <ref>PMID:15601835</ref> <ref>PMID:15687503</ref> <ref>PMID:16076843</ref> <ref>PMID:16109375</ref> <ref>PMID:16630888</ref> <ref>PMID:7877695</ref> <ref>PMID:9702190</ref> <ref>PMID:9845373</ref>
+==See Also==
+*[[Mediator|Mediator]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Z-disk]]
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Boyer TG]]
+[[Category: Chang CE]]
+[[Category: Chao TC]]
+[[Category: Chen SF]]
+[[Category: Cholko T]]
+[[Category: Garcia BA]]
+[[Category: Kim HJ]]
+[[Category: Li YC]]
+[[Category: Murakami K]]
+[[Category: Nakanishi K]]
+[[Category: Tsai KL]]

7kpx: Difference between revisions

Latest revision as of 14:57, 6 March 2024

Structure of the yeast CKM

Structural highlights

Function

See Also

References

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