Entry Database : PDB / ID : 5d6y Structure visualization Downloads & linksTitle Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 ComponentsLysine-specific demethylase 4A peptide H3K23me3 (19-28) DetailsKeywords OXIDOREDUCTASE / double tudor domain / reader domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatProFunction / homology Function and homology informationFunction Domain/homology Component
[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ... [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / Chromatin modifying enzymes / pericentric heterochromatin / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / telomere organization / positive regulation of neuron differentiation / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / negative regulation of autophagy / response to nutrient levels / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / fibrillar center / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / : / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 ... Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / : / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Roll / Roll / Mainly Beta / Alpha Beta Similarity search - Domain/homologyBiological species Homo sapiens (human)Method X-RAY DIFFRACTION / SYNCHROTRON / Resolution : 2.287 Å DetailsAuthors Wang, F. / Su, Z. / Miller, M.D. / Denu, J.M. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) Funding support United States, 2items Details Hide detailsOrganization Grant number Country National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U01GM098248 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 2R37GM059785-15/P250VA United States
CitationJournal : Nat Commun / Year : 2016Title : Reader domain specificity and lysine demethylase-4 family function.Authors: Su, Z. / Wang, F. / Lee, J.H. / Stephens, K.E. / Papazyan, R. / Voronina, E. / Krautkramer, K.A. / Raman, A. / Thorpe, J.J. / Boersma, M.D. / Kuznetsov, V.I. / Miller, M.D. / Taverna, S.D. / ... Authors : Su, Z. / Wang, F. / Lee, J.H. / Stephens, K.E. / Papazyan, R. / Voronina, E. / Krautkramer, K.A. / Raman, A. / Thorpe, J.J. / Boersma, M.D. / Kuznetsov, V.I. / Miller, M.D. / Taverna, S.D. / Phillips, G.N. / Denu, J.M. History Deposition Aug 13, 2015 Deposition site : RCSB / Processing site : RCSBRevision 1.0 Feb 10, 2016 Provider : repository / Type : Initial releaseRevision 1.1 Dec 7, 2016 Group : Database referencesRevision 1.2 Sep 20, 2017 Group : Author supporting evidence / Category : pdbx_audit_support / Item : _pdbx_audit_support.funding_organizationRevision 1.3 Dec 25, 2019 Group : Author supporting evidence / Category : pdbx_audit_support / Item : _pdbx_audit_support.funding_organization
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