View source for 5btr


==Crystal structure of SIRT1 in complex with resveratrol and an AMC-containing peptide==
<StructureSection load='5btr' size='340' side='right'caption='[[5btr]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5btr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=5BTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BTR 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]] 3.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=FDL:N~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE'>FDL</scene>, <scene name='pdbligand=STL:RESVERATROL'>STL</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=5btr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5btr OCA], [https://pdbe.org/5btr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5btr RCSB], [https://www.ebi.ac.uk/pdbsum/5btr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5btr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SIR1_HUMAN SIR1_HUMAN] NAD-dependent protein deacetylase that links transcriptional regulation directly to intracellular energetics and participates in the coordination of several separated cellular functions such as cell cycle, response to DNA damage, metobolism, apoptosis and autophagy. Can modulate chromatin function through deacetylation of histones and can promote alterations in the methylation of histones and DNA, leading to transcriptional repression. Deacetylates a broad range of transcription factors and coregulators, thereby regulating target gene expression positively and negatively. Serves as a sensor of the cytosolic ratio of NAD(+)/NADH which is altered by glucose deprivation and metabolic changes associated with caloric restriction. Is essential in skeletal muscle cell differentiation and in response to low nutrients mediates the inhibitory effect on skeletal myoblast differentiation which also involves 5'-AMP-activated protein kinase (AMPK) and nicotinamide phosphoribosyltransferase (NAMPT). Component of the eNoSC (energy-dependent nucleolar silencing) complex, a complex that mediates silencing of rDNA in response to intracellular energy status and acts by recruiting histone-modifying enzymes. The eNoSC complex is able to sense the energy status of cell: upon glucose starvation, elevation of NAD(+)/NADP(+) ratio activates SIRT1, leading to histone H3 deacetylation followed by dimethylation of H3 at 'Lys-9' (H3K9me2) by SUV39H1 and the formation of silent chromatin in the rDNA locus. Deacetylates 'Lys-266' of SUV39H1, leading to its activation. Inhibits skeletal muscle differentiation by deacetylating PCAF and MYOD1. Deacetylates H2A and 'Lys-26' of HIST1H1E. Deacetylates 'Lys-16' of histone H4 (in vitro). Involved in NR0B2/SHP corepression function through chromatin remodeling: Recruited to LRH1 target gene promoters by NR0B2/SHP thereby stimulating histone H3 and H4 deacetylation leading to transcriptional repression. Proposed to contribute to genomic integrity via positive regulation of telomere length; however, reports on localization to pericentromeric heterochromatin are conflicting. Proposed to play a role in constitutive heterochromatin (CH) formation and/or maintenance through regulation of the available pool of nuclear SUV39H1. Upon oxidative/metabolic stress decreases SUV39H1 degradation by inhibiting SUV39H1 polyubiquitination by MDM2. This increase in SUV39H1 levels enhances SUV39H1 turnover in CH, which in turn seems to accelerate renewal of the heterochromatin which correlates with greater genomic integrity during stress response. Deacetylates 'Lys-382' of p53/TP53 and impairs its ability to induce transcription-dependent proapoptotic program and modulate cell senescence. Deacetylates TAF1B and thereby represses rDNA transcription by the RNA polymerase I. Deacetylates MYC, promotes the association of MYC with MAX and decreases MYC stability leading to compromised transformational capability. Deacetylates FOXO3 in response to oxidative stress thereby increasing its ability to induce cell cycle arrest and resistance to oxidative stress but inhibiting FOXO3-mediated induction of apoptosis transcriptional activity; also leading to FOXO3 ubiquitination and protesomal degradation. Appears to have a similar effect on MLLT7/FOXO4 in regulation of transcriptional activity and apoptosis. Deacetylates DNMT1; thereby impairs DNMT1 methyltransferase-independent transcription repressor activity, modulates DNMT1 cell cycle regulatory function and DNMT1-mediated gene silencing. Deacetylates RELA/NF-kappa-B p65 thereby inhibiting its transactivating potential and augments apoptosis in response to TNF-alpha. Deacetylates HIF1A, KAT5/TIP60, RB1 and HIC1. Deacetylates FOXO1 resulting in its nuclear retention and enhancement of its transcriptional activity leading to increased gluconeogenesis in liver. Inhibits E2F1 transcriptional activity and apoptotic function, possibly by deacetylation. Involved in HES1- and HEY2-mediated transcriptional repression. In cooperation with MYCN seems to be involved in transcriptional repression of DUSP6/MAPK3 leading to MYCN stabilization by phosphorylation at 'Ser-62'. Deacetylates MEF2D. Required for antagonist-mediated transcription suppression of AR-dependent genes which may be linked to local deacetylation of histone H3. Represses HNF1A-mediated transcription. Required for the repression of ESRRG by CREBZF. Modulates AP-1 transcription factor activity. Deacetylates NR1H3 AND NR1H2 and deacetylation of NR1H3 at 'Lys-434' positively regulates transcription of NR1H3:RXR target genes, promotes NR1H3 proteosomal degradation and results in cholesterol efflux; a promoter clearing mechanism after reach round of transcription is proposed. Involved in lipid metabolism. Implicated in regulation of adipogenesis and fat mobilization in white adipocytes by repression of PPARG which probably involves association with NCOR1 and SMRT/NCOR2. Deacetylates ACSS2 leading to its activation, and HMGCS1. Involved in liver and muscle metabolism. Through deacteylation and activation of PPARGC1A is required to activate fatty acid oxidation in skeletel muscle under low-glucose conditions and is involved in glucose homeostasis. Involved in regulation of PPARA and fatty acid beta-oxidation in liver. Involved in positive regulation of insulin secretion in pancreatic beta cells in response to glucose; the function seems to imply transcriptional repression of UCP2. Proposed to deacetylate IRS2 thereby facilitating its insuline-induced tyrosine phosphorylation. Deacetylates SREBF1 isoform SREBP-1C thereby decreasing its stability and transactivation in lipogenic gene expression. Involved in DNA damage response by repressing genes which are involved in DNA repair, such as XPC and TP73, deacetylating XRCC6/Ku70, and faciliting recruitment of additional factors to sites of damaged DNA, such as SIRT1-deacetylated NBN can recruit ATM to initiate DNA repair and SIRT1-deacetylated XPA interacts with RPA2. Also involved in DNA repair of DNA double-strand breaks by homologous recombination and specifically single-strand annealing independently of XRCC6/Ku70 and NBN. Transcriptional suppression of XPC probably involves an E2F4:RBL2 suppressor complex and protein kinase B (AKT) signaling. Transcriptional suppression of TP73 probably involves E2F4 and PCAF. Deacetylates WRN thereby regulating its helicase and exonuclease activities and regulates WRN nuclear translocation in response to DNA damage. Deacetylates APEX1 at 'Lys-6' and 'Lys-7' and stimulates cellular AP endonuclease activity by promoting the association of APEX1 to XRCC1. Increases p53/TP53-mediated transcription-independent apoptosis by blocking nuclear translocation of cytoplasmic p53/TP53 and probably redirecting it to mitochondria. Deacetylates XRCC6/Ku70 at 'Lys-539' and 'Lys-542' causing it to sequester BAX away from mitochondria thereby inhibiting stress-induced apoptosis. Is involved in autophagy, presumably by deacetylating ATG5, ATG7 and MAP1LC3B/ATG8. Deacetylates AKT1 which leads to enhanced binding of AKT1 and PDK1 to PIP3 and promotes their activation. Proposed to play role in regulation of STK11/LBK1-dependent AMPK signaling pathways implicated in cellular senescence which seems to involve the regulation of the acetylation status of STK11/LBK1. Can deacetylate STK11/LBK1 and thereby increase its activity, cytoplasmic localization and association with STRAD; however, the relevance of such activity in normal cells is unclear. In endothelial cells is shown to inhibit STK11/LBK1 activity and to promote its degradation. Deacetylates SMAD7 at 'Lys-64' and 'Lys-70' thereby promoting its degradation. Deacetylates CIITA and augments its MHC class II transacivation and contributes to its stability. Deacteylates MECOM/EVI1. Isoform 2 is shown to deacetylate 'Lys-382' of p53/TP53, however with lower activity than isoform 1. In combination, the two isoforms exert an additive effect. Isoform 2 regulates p53/TP53 expression and cellular stress response and is in turn repressed by p53/TP53 presenting a SIRT1 isoform-dependent auto-regulatory loop. In case of HIV-1 infection, interacts with and deacetylates the viral Tat protein. The viral Tat protein inhibits SIRT1 deacetylation activity toward RELA/NF-kappa-B p65, thereby potentiates its transcriptional activity and SIRT1 is proposed to contribute to T-cell hyperactivation during infection. Deacetylates PML at 'Lys-487' and this deacetylation promotes PML control of PER2 nuclear localization.<ref>PMID:11672523</ref> <ref>PMID:12006491</ref> <ref>PMID:15152190</ref> <ref>PMID:14980222</ref> <ref>PMID:15126506</ref> <ref>PMID:15469825</ref> <ref>PMID:14976264</ref> <ref>PMID:15205477</ref> <ref>PMID:15692560</ref> <ref>PMID:16079181</ref> <ref>PMID:16166628</ref> <ref>PMID:16892051</ref> <ref>PMID:17620057</ref> <ref>PMID:17334224</ref> <ref>PMID:16998810</ref> <ref>PMID:17505061</ref> <ref>PMID:17936707</ref> <ref>PMID:17612497</ref> <ref>PMID:17283066</ref> <ref>PMID:18485871</ref> <ref>PMID:18329615</ref> <ref>PMID:18203716</ref> <ref>PMID:18687677</ref> <ref>PMID:18296641</ref> <ref>PMID:19220062</ref> <ref>PMID:19690166</ref> <ref>PMID:19364925</ref> <ref>PMID:19188449</ref> <ref>PMID:20203304</ref> <ref>PMID:20097625</ref> <ref>PMID:20100829</ref> <ref>PMID:20817729</ref> <ref>PMID:20620956</ref> <ref>PMID:20670893</ref> <ref>PMID:19934257</ref> <ref>PMID:20375098</ref> <ref>PMID:20975832</ref> <ref>PMID:21149730</ref> <ref>PMID:21701047</ref> <ref>PMID:21555002</ref> <ref>PMID:21807113</ref> <ref>PMID:21471201</ref> <ref>PMID:21504832</ref> <ref>PMID:21947282</ref> <ref>PMID:21698133</ref> <ref>PMID:21775285</ref> <ref>PMID:21987377</ref> <ref>PMID:21890893</ref> <ref>PMID:22274616</ref> <ref>PMID:21841822</ref>   SirtT1 75 kDa fragment: catalytically inactive 75SirT1 may be involved in regulation of apoptosis. May be involved in protecting chondrocytes from apoptotic death by associating with cytochrome C and interfering with apoptosome assembly.<ref>PMID:11672523</ref> <ref>PMID:12006491</ref> <ref>PMID:15152190</ref> <ref>PMID:14980222</ref> <ref>PMID:15126506</ref> <ref>PMID:15469825</ref> <ref>PMID:14976264</ref> <ref>PMID:15205477</ref> <ref>PMID:15692560</ref> <ref>PMID:16079181</ref> <ref>PMID:16166628</ref> <ref>PMID:16892051</ref> <ref>PMID:17620057</ref> <ref>PMID:17334224</ref> <ref>PMID:16998810</ref> <ref>PMID:17505061</ref> <ref>PMID:17936707</ref> <ref>PMID:17612497</ref> <ref>PMID:17283066</ref> <ref>PMID:18485871</ref> <ref>PMID:18329615</ref> <ref>PMID:18203716</ref> <ref>PMID:18687677</ref> <ref>PMID:18296641</ref> <ref>PMID:19220062</ref> <ref>PMID:19690166</ref> <ref>PMID:19364925</ref> <ref>PMID:19188449</ref> <ref>PMID:20203304</ref> <ref>PMID:20097625</ref> <ref>PMID:20100829</ref> <ref>PMID:20817729</ref> <ref>PMID:20620956</ref> <ref>PMID:20670893</ref> <ref>PMID:19934257</ref> <ref>PMID:20375098</ref> <ref>PMID:20975832</ref> <ref>PMID:21149730</ref> <ref>PMID:21701047</ref> <ref>PMID:21555002</ref> <ref>PMID:21807113</ref> <ref>PMID:21471201</ref> <ref>PMID:21504832</ref> <ref>PMID:21947282</ref> <ref>PMID:21698133</ref> <ref>PMID:21775285</ref> <ref>PMID:21987377</ref> <ref>PMID:21890893</ref> <ref>PMID:22274616</ref> <ref>PMID:21841822</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Sirtuins with an extended N-terminal domain (NTD), represented by yeast Sir2 and human SIRT1, harbor intrinsic mechanisms for regulation of their NAD-dependent deacetylase activities. Elucidation of the regulatory mechanisms is crucial for understanding the biological functions of sirtuins and development of potential therapeutics. In particular, SIRT1 has emerged as an attractive therapeutic target, and the search for SIRT1-activating compounds (STACs) has been actively pursued. However, the effectiveness of a class of reported STACs (represented by resveratrol) as direct SIRT1 activators is under debate due to the complication involving the use of fluorogenic substrates in in vitro assays. Future efforts of SIRT1-based therapeutics necessitate the dissection of the molecular mechanism of SIRT1 stimulation. We solved the structure of SIRT1 in complex with resveratrol and a 7-amino-4-methylcoumarin (AMC)-containing peptide. The structure reveals the presence of three resveratrol molecules, two of which mediate the interaction between the AMC peptide and the NTD of SIRT1. The two NTD-bound resveratrol molecules are principally responsible for promoting tighter binding between SIRT1 and the peptide and the stimulation of SIRT1 activity. The structural information provides valuable insights into regulation of SIRT1 activity and should benefit the development of authentic SIRT1 activators.

Structural basis for allosteric, substrate-dependent stimulation of SIRT1 activity by resveratrol.,Cao D, Wang M, Qiu X, Liu D, Jiang H, Yang N, Xu RM Genes Dev. 2015 Jun 15;29(12):1316-25. doi: 10.1101/gad.265462.115. PMID:26109052<ref>PMID:26109052</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5btr" style="background-color:#fffaf0;"></div>

==See Also==
*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Cao D]]
[[Category: Jiang H]]
[[Category: Liu D]]
[[Category: Qiu X]]
[[Category: Wang M]]
[[Category: Xu RM]]
[[Category: Yang N]]