Entry Database : PDB / ID : 4i5i Structure visualization Downloads & linksTitle Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog ComponentsNAD-dependent protein deacetylase sirtuin-1 Details Keywords HYDROLASE / Rossmann Fold / histone deacetylase / epigenetics / cancer / sirtuin / acetylated lysine of histoneFunction / homology Function and homology informationFunction Domain/homology Component
negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / eNoSc complex / histone H4K12 deacetylase activity / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / protein depropionylation ... negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / eNoSc complex / histone H4K12 deacetylase activity / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / protein depropionylation / protein-propionyllysine depropionylase activity / regulation of peroxisome proliferator activated receptor signaling pathway / regulation of transcription by glucose / regulation of protein serine/threonine kinase activity / Regulation of MITF-M dependent genes involved in metabolism / positive regulation of macrophage apoptotic process / NAD-dependent histone H3K14 deacetylase activity / negative regulation of triglyceride biosynthetic process / regulation of endodeoxyribonuclease activity / triglyceride mobilization / behavioral response to starvation / pyrimidine dimer repair by nucleotide-excision repair / keratin filament binding / HLH domain binding / regulation of lipid storage / NAD-dependent histone H3K9 deacetylase activity / leptin-mediated signaling pathway / negative regulation of peptidyl-lysine acetylation / NAD-dependent histone H4K16 deacetylase activity / deacetylase activity / regulation of brown fat cell differentiation / positive regulation of smooth muscle cell differentiation / bHLH transcription factor binding / response to leptin / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / intracellular triglyceride homeostasis / peptidyl-lysine acetylation / negative regulation of androgen receptor signaling pathway / positive regulation of adaptive immune response / regulation of centrosome duplication / rDNA heterochromatin / ovulation from ovarian follicle / single strand break repair / negative regulation of cAMP-dependent protein kinase activity / regulation of bile acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / negative regulation of signal transduction by p53 class mediator / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / negative regulation of protein acetylation / negative regulation of phosphorylation / chromatin silencing complex / NAD-dependent histone deacetylase activity / DNA methylation-dependent heterochromatin formation / protein deacetylation / positive regulation of MHC class II biosynthetic process / UV-damage excision repair / protein lysine deacetylase activity / positive regulation of cAMP-dependent protein kinase activity / negative regulation of TOR signaling / negative regulation of helicase activity / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / Regulation of FOXO transcriptional activity by acetylation / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / nuclear inner membrane / muscle organ development / stress-induced premature senescence / histone deacetylase activity / negative regulation of NF-kappaB transcription factor activity / DNA synthesis involved in DNA repair / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of fat cell differentiation / intracellular glucose homeostasis / negative regulation of cellular senescence / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of DNA damage response, signal transduction by p53 class mediator / macrophage differentiation / positive regulation of macroautophagy / negative regulation of cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / white fat cell differentiation / regulation of glucose metabolic process / NAD+ binding / Regulation of HSF1-mediated heat shock response / positive regulation of cholesterol efflux / positive regulation of blood vessel endothelial cell migration / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / fatty acid homeostasis / heterochromatin / energy homeostasis / cellular response to glucose starvation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of cellular response to heat / positive regulation of insulin receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of gluconeogenesis / positive regulation of endothelial cell proliferation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function : / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ... : / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homologyBiological species Homo sapiens (human)Method X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution : 2.5 Å DetailsAuthors Zhao, X. / Allison, D. / Condon, B. / Zhang, F. / Gheyi, T. / Zhang, A. / Ashok, S. / Russell, M. / Macewan, I. / Qian, Y. ...Zhao, X. / Allison, D. / Condon, B. / Zhang, F. / Gheyi, T. / Zhang, A. / Ashok, S. / Russell, M. / Macewan, I. / Qian, Y. / Jamison, J.A. / Luz, J.G. CitationJournal : J.Med.Chem. / Year : 2013Title : The 2.5 angstrom crystal structure of the SIRT1 catalytic domain bound to nicotinamide adenine dinucleotide (NAD+) and an indole (EX527 analogue) reveals a novel mechanism of histone deacetylase inhibition.Authors : Zhao, X. / Allison, D. / Condon, B. / Zhang, F. / Gheyi, T. / Zhang, A. / Ashok, S. / Russell, M. / MacEwan, I. / Qian, Y. / Jamison, J.A. / Luz, J.G. History Deposition Nov 28, 2012 Deposition site : RCSB / Processing site : RCSBRevision 1.0 Jan 23, 2013 Provider : repository / Type : Initial releaseRevision 1.1 Aug 28, 2013 Group : Database referencesRevision 1.2 Nov 12, 2014 Group : Structure summaryRevision 1.3 Sep 20, 2023 Group : Data collection / Database references ... Data collection / Database references / Derived calculations / Refinement description Category : chem_comp_atom / chem_comp_bond ... chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item : _database_2.pdbx_DOI / _database_2.pdbx_database_accession ... _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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