3q33: Difference between revisions

Latest revision as of 10:20, 6 November 2024

Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation

Structural highlights

3q33 is a 3 chain structure with sequence from Saccharomyces cerevisiae and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	ACO, ALY, EDO, NH2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RT109_YEAST Required for acetylation of 'Lys-56' of histone H3 (H3K56ac) which occurs in S phase and disappears during G(2)/M phase of the cell cycle and is involved in transcription DNA repair process. H3K56 acetylation weakens of the interaction between the histone core and the surrounding DNA in the nucleosomal particle and drives chromatin disassembly. Involved in regulation of Ty1 transposition.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Yeast Rtt109 promotes nucleosome assembly and genome stability by acetylating K9, K27, and K56 of histone H3 through interaction with either of two distinct histone chaperones, Vps75 or Asf1. We report the crystal structure of an Rtt109-AcCoA/Vps75 complex revealing an elongated Vps75 homodimer bound to two globular Rtt109 molecules to form a symmetrical holoenzyme with a approximately 12 A diameter central hole. Vps75 and Rtt109 residues that mediate complex formation in the crystals are also important for Rtt109-Vps75 interaction and H3K9/K27 acetylation both in vitro and in yeast cells. The same Rtt109 residues do not participate in Asf1-mediated Rtt109 acetylation in vitro or H3K56 acetylation in yeast cells, demonstrating that Asf1 and Vps75 dictate Rtt109 substrate specificity through distinct mechanisms. These studies also suggest that Vps75 binding stimulates Rtt109 catalytic activity by appropriately presenting the H3-H4 substrate within the central cavity of the holoenzyme to promote H3K9/K27 acetylation of new histones before deposition.

Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation.,Tang Y, Holbert MA, Delgoshaie N, Wurtele H, Guillemette B, Meeth K, Yuan H, Drogaris P, Lee EH, Durette C, Thibault P, Verreault A, Cole PA, Marmorstein R Structure. 2011 Feb 9;19(2):221-31. Epub 2011 Jan 20. PMID:21256037^[10]

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

References

↑ Scholes DT, Banerjee M, Bowen B, Curcio MJ. Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics. 2001 Dec;159(4):1449-65. PMID:11779788
↑ Schneider J, Bajwa P, Johnson FC, Bhaumik SR, Shilatifard A. Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J Biol Chem. 2006 Dec 8;281(49):37270-4. Epub 2006 Oct 17. PMID:17046836 doi:https://dx.doi.org/10.1074/jbc.C600265200
↑ Han J, Zhou H, Li Z, Xu RM, Zhang Z. The Rtt109-Vps75 histone acetyltransferase complex acetylates non-nucleosomal histone H3. J Biol Chem. 2007 May 11;282(19):14158-64. Epub 2007 Mar 16. PMID:17369253 doi:https://dx.doi.org/10.1074/jbc.M700611200
↑ Han J, Zhou H, Li Z, Xu RM, Zhang Z. Acetylation of lysine 56 of histone H3 catalyzed by RTT109 and regulated by ASF1 is required for replisome integrity. J Biol Chem. 2007 Sep 28;282(39):28587-96. Epub 2007 Aug 9. PMID:17690098 doi:https://dx.doi.org/10.1074/jbc.M702496200
↑ Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, Denu JM, Kaufman PD. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell. 2007 Mar 9;25(5):703-12. Epub 2007 Feb 22. PMID:17320445 doi:S1097-2765(07)00086-X
↑ Driscoll R, Hudson A, Jackson SP. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science. 2007 Feb 2;315(5812):649-52. PMID:17272722 doi:https://dx.doi.org/315/5812/649
↑ Han J, Zhou H, Horazdovsky B, Zhang K, Xu RM, Zhang Z. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science. 2007 Feb 2;315(5812):653-5. PMID:17272723 doi:https://dx.doi.org/10.1126/science.1133234
↑ Williams SK, Truong D, Tyler JK. Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation. Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9000-5. doi:, 10.1073/pnas.0800057105. Epub 2008 Jun 24. PMID:18577595 doi:https://dx.doi.org/10.1073/pnas.0800057105
↑ Tang Y, Meeth K, Jiang E, Luo C, Marmorstein R. Structure of Vps75 and implications for histone chaperone function. Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12206-11. Epub 2008 Aug 22. PMID:18723682
↑ Tang Y, Holbert MA, Delgoshaie N, Wurtele H, Guillemette B, Meeth K, Yuan H, Drogaris P, Lee EH, Durette C, Thibault P, Verreault A, Cole PA, Marmorstein R. Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation. Structure. 2011 Feb 9;19(2):221-31. Epub 2011 Jan 20. PMID:21256037 doi:10.1016/j.str.2010.12.012

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Scholes DT, Banerjee M, Bowen B, Curcio MJ. Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics. 2001 Dec;159(4):1449-65. PMID:11779788

[2] Schneider J, Bajwa P, Johnson FC, Bhaumik SR, Shilatifard A. Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J Biol Chem. 2006 Dec 8;281(49):37270-4. Epub 2006 Oct 17. PMID:17046836 doi:https://dx.doi.org/10.1074/jbc.C600265200

[3] Han J, Zhou H, Li Z, Xu RM, Zhang Z. The Rtt109-Vps75 histone acetyltransferase complex acetylates non-nucleosomal histone H3. J Biol Chem. 2007 May 11;282(19):14158-64. Epub 2007 Mar 16. PMID:17369253 doi:https://dx.doi.org/10.1074/jbc.M700611200

[4] Han J, Zhou H, Li Z, Xu RM, Zhang Z. Acetylation of lysine 56 of histone H3 catalyzed by RTT109 and regulated by ASF1 is required for replisome integrity. J Biol Chem. 2007 Sep 28;282(39):28587-96. Epub 2007 Aug 9. PMID:17690098 doi:https://dx.doi.org/10.1074/jbc.M702496200

[5] Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, Denu JM, Kaufman PD. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell. 2007 Mar 9;25(5):703-12. Epub 2007 Feb 22. PMID:17320445 doi:S1097-2765(07)00086-X

[6] Driscoll R, Hudson A, Jackson SP. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science. 2007 Feb 2;315(5812):649-52. PMID:17272722 doi:https://dx.doi.org/315/5812/649

[7] Han J, Zhou H, Horazdovsky B, Zhang K, Xu RM, Zhang Z. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science. 2007 Feb 2;315(5812):653-5. PMID:17272723 doi:https://dx.doi.org/10.1126/science.1133234

[8] Williams SK, Truong D, Tyler JK. Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation. Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9000-5. doi:, 10.1073/pnas.0800057105. Epub 2008 Jun 24. PMID:18577595 doi:https://dx.doi.org/10.1073/pnas.0800057105

[9] Tang Y, Meeth K, Jiang E, Luo C, Marmorstein R. Structure of Vps75 and implications for histone chaperone function. Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12206-11. Epub 2008 Aug 22. PMID:18723682

[10] Tang Y, Holbert MA, Delgoshaie N, Wurtele H, Guillemette B, Meeth K, Yuan H, Drogaris P, Lee EH, Durette C, Thibault P, Verreault A, Cole PA, Marmorstein R. Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation. Structure. 2011 Feb 9;19(2):221-31. Epub 2011 Jan 20. PMID:21256037 doi:10.1016/j.str.2010.12.012

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[3]

[4]

[5]

[6]

[7]

[8]

[9]

[10]

@@ Line 3: / Line 3: @@
 <StructureSection load='3q33' size='340' side='right'caption='[[3q33]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3q33]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q33 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3q33]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q33 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3d35|3d35]], [[3dm7|3dm7]], [[3q35|3q35]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KIM2, L1377, REM50, RTT109, SCY_3578, YLL002W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), N0890, VPS75, YNL246W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=3q33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q33 OCA], [https://pdbe.org/3q33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q33 RCSB], [https://www.ebi.ac.uk/pdbsum/3q33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q33 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RT109_YEAST RT109_YEAST]] Required for acetylation of 'Lys-56' of histone H3 (H3K56ac) which occurs in S phase and disappears during G(2)/M phase of the cell cycle and is involved in transcription DNA repair process. H3K56 acetylation weakens of the interaction between the histone core and the surrounding DNA in the nucleosomal particle and drives chromatin disassembly. Involved in regulation of Ty1 transposition.<ref>PMID:11779788</ref> <ref>PMID:17046836</ref> <ref>PMID:17369253</ref> <ref>PMID:17690098</ref> <ref>PMID:17320445</ref> <ref>PMID:17272722</ref> <ref>PMID:17272723</ref> <ref>PMID:18577595</ref> <ref>PMID:18723682</ref>  [[https://www.uniprot.org/uniprot/VPS75_YEAST VPS75_YEAST]] Histone chaperone which acts as a cofactor stimulating the histone H3 'Lys-56' acetylation by RTT109. May be involved in vacuolar proteins sorting.<ref>PMID:12134085</ref> <ref>PMID:17320445</ref>
+[https://www.uniprot.org/uniprot/RT109_YEAST RT109_YEAST] Required for acetylation of 'Lys-56' of histone H3 (H3K56ac) which occurs in S phase and disappears during G(2)/M phase of the cell cycle and is involved in transcription DNA repair process. H3K56 acetylation weakens of the interaction between the histone core and the surrounding DNA in the nucleosomal particle and drives chromatin disassembly. Involved in regulation of Ty1 transposition.<ref>PMID:11779788</ref> <ref>PMID:17046836</ref> <ref>PMID:17369253</ref> <ref>PMID:17690098</ref> <ref>PMID:17320445</ref> <ref>PMID:17272722</ref> <ref>PMID:17272723</ref> <ref>PMID:18577595</ref> <ref>PMID:18723682</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 30: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
-[[Category: Histone acetyltransferase]]
 [[Category: Large Structures]]
-[[Category: Marmorstein, R]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Meeth, K]]
+[[Category: Synthetic construct]]
-[[Category: Tang, Y]]
+[[Category: Marmorstein R]]
-[[Category: Yuan, H]]
+[[Category: Meeth K]]
-[[Category: Autoacetylation on rtt109 lys290]]
+[[Category: Tang Y]]
-[[Category: Chaperone-gene regulation complex]]
+[[Category: Yuan H]]
-[[Category: Nuclear]]
-[[Category: Rtt109:vps75=2:2 stoichiometry complex]]
-[[Category: Transferase]]
-[[Category: Transferase-chaperone complex]]
-[[Category: Transferase-chaperone-transcription regulator complex]]

3q33: Difference between revisions

Latest revision as of 10:20, 6 November 2024

Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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