7f51: Difference between revisions

Latest revision as of 17:09, 29 November 2023

Crystal structure of Hst2 in complex with 2'-O-Benzoyl ADP Ribose

Structural highlights

7f51 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 1.98Å
Ligands:	BA7, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HST2_YEAST NAD-dependent histone deacetylase that is involved in nuclear silencing events. Derepresses subtelomeric silencing and increases repression in nucleolar (rDNA) silencing. Its function is negatively regulated by active nuclear export.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Lysine benzoylation (Kbz) is a recently discovered post-translational modification associated with active transcription. However, the proteins for maintaining and interpreting Kbz and the physiological roles of Kbz remain elusive. Here, we systematically characterize writer, eraser, and reader proteins of histone Kbz in S. cerevisiae using proteomic, biochemical, and structural approaches. Our study identifies 27 Kbz sites on yeast histones that can be regulated by cellular metabolic states. The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex and NAD(+)-dependent histone deacetylase Hst2 could function as the writer and eraser of histone Kbz, respectively. Crystal structures of Hst2 complexes reveal the molecular basis for Kbz recognition and catalysis by Hst2. In addition, we demonstrate that a subset of YEATS domains and bromodomains serve as Kbz readers, and structural analyses reveal how YEATS and bromodomains recognize Kbz marks. Moreover, the proteome-wide screening of Kbz-modified proteins identifies 207 Kbz sites on 149 non-histone proteins enriched in ribosome biogenesis, glycolysis/gluconeogenesis, and rRNA processing pathways. Our studies identify regulatory elements for the Kbz pathway and provide a framework for dissecting the biological functions of lysine benzoylation.

Global profiling of regulatory elements in the histone benzoylation pathway.,Wang D, Yan F, Wu P, Ge K, Li M, Li T, Gao Y, Peng C, Chen Y Nat Commun. 2022 Mar 16;13(1):1369. doi: 10.1038/s41467-022-29057-2. PMID:35296687^[6]

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

References

↑ Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus L, Sternglanz R. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci U S A. 2000 May 23;97(11):5807-11. PMID:10811920 doi:https://dx.doi.org/10.1073/pnas.110148297
↑ Tanner KG, Landry J, Sternglanz R, Denu JM. Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14178-82. PMID:11106374 doi:https://dx.doi.org/10.1073/pnas.250422697
↑ Perrod S, Cockell MM, Laroche T, Renauld H, Ducrest AL, Bonnard C, Gasser SM. A cytosolic NAD-dependent deacetylase, Hst2p, can modulate nucleolar and telomeric silencing in yeast. EMBO J. 2001 Jan 15;20(1-2):197-209. PMID:11226170 doi:https://dx.doi.org/10.1093/emboj/20.1.197
↑ Borra MT, Langer MR, Slama JT, Denu JM. Substrate specificity and kinetic mechanism of the Sir2 family of NAD+-dependent histone/protein deacetylases. Biochemistry. 2004 Aug 3;43(30):9877-87. PMID:15274642 doi:https://dx.doi.org/10.1021/bi049592e
↑ Wilson JM, Le VQ, Zimmerman C, Marmorstein R, Pillus L. Nuclear export modulates the cytoplasmic Sir2 homologue Hst2. EMBO Rep. 2006 Dec;7(12):1247-51. Epub 2006 Nov 17. PMID:17110954 doi:https://dx.doi.org/10.1038/sj.embor.7400829
↑ Wang D, Yan F, Wu P, Ge K, Li M, Li T, Gao Y, Peng C, Chen Y. Global profiling of regulatory elements in the histone benzoylation pathway. Nat Commun. 2022 Mar 16;13(1):1369. doi: 10.1038/s41467-022-29057-2. PMID:35296687 doi:https://dx.doi.org/10.1038/s41467-022-29057-2

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Landry J, Sutton A, Tafrov ST, Heller RC, Stebbins J, Pillus L, Sternglanz R. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc Natl Acad Sci U S A. 2000 May 23;97(11):5807-11. PMID:10811920 doi:https://dx.doi.org/10.1073/pnas.110148297

[2] Tanner KG, Landry J, Sternglanz R, Denu JM. Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14178-82. PMID:11106374 doi:https://dx.doi.org/10.1073/pnas.250422697

[3] Perrod S, Cockell MM, Laroche T, Renauld H, Ducrest AL, Bonnard C, Gasser SM. A cytosolic NAD-dependent deacetylase, Hst2p, can modulate nucleolar and telomeric silencing in yeast. EMBO J. 2001 Jan 15;20(1-2):197-209. PMID:11226170 doi:https://dx.doi.org/10.1093/emboj/20.1.197

[4] Borra MT, Langer MR, Slama JT, Denu JM. Substrate specificity and kinetic mechanism of the Sir2 family of NAD+-dependent histone/protein deacetylases. Biochemistry. 2004 Aug 3;43(30):9877-87. PMID:15274642 doi:https://dx.doi.org/10.1021/bi049592e

[5] Wilson JM, Le VQ, Zimmerman C, Marmorstein R, Pillus L. Nuclear export modulates the cytoplasmic Sir2 homologue Hst2. EMBO Rep. 2006 Dec;7(12):1247-51. Epub 2006 Nov 17. PMID:17110954 doi:https://dx.doi.org/10.1038/sj.embor.7400829

[6] Wang D, Yan F, Wu P, Ge K, Li M, Li T, Gao Y, Peng C, Chen Y. Global profiling of regulatory elements in the histone benzoylation pathway. Nat Commun. 2022 Mar 16;13(1):1369. doi: 10.1038/s41467-022-29057-2. PMID:35296687 doi:https://dx.doi.org/10.1038/s41467-022-29057-2

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[2]

[3]

[4]

[5]

[6]

@@ Line 3: / Line 3: @@
 <StructureSection load='7f51' size='340' side='right'caption='[[7f51]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7f51]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F51 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F51 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7f51]] 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=7F51 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F51 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA7:[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl]+benzoate'>BA7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.98&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein_acetyllysine_N-acetyltransferase Protein acetyllysine N-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.286 2.3.1.286] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA7:[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl]+benzoate'>BA7</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7f51 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f51 OCA], [https://pdbe.org/7f51 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f51 RCSB], [https://www.ebi.ac.uk/pdbsum/7f51 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f51 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/HST2_YEAST HST2_YEAST]] NAD-dependent histone deacetylase that is involved in nuclear silencing events. Derepresses subtelomeric silencing and increases repression in nucleolar (rDNA) silencing. Its function is negatively regulated by active nuclear export.<ref>PMID:10811920</ref> <ref>PMID:11106374</ref> <ref>PMID:11226170</ref> <ref>PMID:15274642</ref> <ref>PMID:17110954</ref>
+[https://www.uniprot.org/uniprot/HST2_YEAST HST2_YEAST] NAD-dependent histone deacetylase that is involved in nuclear silencing events. Derepresses subtelomeric silencing and increases repression in nucleolar (rDNA) silencing. Its function is negatively regulated by active nuclear export.<ref>PMID:10811920</ref> <ref>PMID:11106374</ref> <ref>PMID:11226170</ref> <ref>PMID:15274642</ref> <ref>PMID:17110954</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Protein acetyllysine N-acetyltransferase]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Chen, Y]]
+[[Category: Chen Y]]
-[[Category: Wang, D]]
+[[Category: Wang D]]
-[[Category: Yan, F]]
+[[Category: Yan F]]
-[[Category: Histone benzoylation]]
-[[Category: Histone modification]]
-[[Category: Nad-dependent histone deacetylase]]
-[[Category: Nuclear protein]]
-[[Category: Protein-protein interaction]]

7f51: Difference between revisions

Latest revision as of 17:09, 29 November 2023

Crystal structure of Hst2 in complex with 2'-O-Benzoyl ADP Ribose

Structural highlights

Function

Publication Abstract from PubMed

References

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