ID PHF2_HUMAN Reviewed; 1096 AA. AC O75151; Q4VXG0; Q8N3K2; Q9Y6N4; DT 15-AUG-2003, integrated into UniProtKB/Swiss-Prot. DT 25-NOV-2008, sequence version 4. DT 27-MAR-2024, entry version 175. DE RecName: Full=Lysine-specific demethylase PHF2; DE EC=1.14.11.- {ECO:0000269|PubMed:21532585}; DE AltName: Full=GRC5; DE AltName: Full=PHD finger protein 2; GN Name=PHF2 {ECO:0000312|HGNC:HGNC:8920}; GN Synonyms=CENP-35 {ECO:0000303|PubMed:20813266}, KIAA0662; OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. OX NCBI_TaxID=9606; RN [1] RP NUCLEOTIDE SEQUENCE [MRNA]. RX PubMed=10051327; DOI=10.1007/s003359900989; RA Hasenpusch-Theil K., Chadwick B.P., Theil T., Heath S.K., Wilkinson D.G., RA Frischauf A.M.; RT "PHF2, a novel PHD finger gene located on human chromosome 9q22."; RL Mamm. Genome 10:294-298(1999). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. RC TISSUE=Brain; RX PubMed=9734811; DOI=10.1093/dnares/5.3.169; RA Ishikawa K., Nagase T., Suyama M., Miyajima N., Tanaka A., Kotani H., RA Nomura N., Ohara O.; RT "Prediction of the coding sequences of unidentified human genes. X. The RT complete sequences of 100 new cDNA clones from brain which can code for RT large proteins in vitro."; RL DNA Res. 5:169-176(1998). RN [3] RP SEQUENCE REVISION. RX PubMed=12168954; DOI=10.1093/dnares/9.3.99; RA Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.; RT "Construction of expression-ready cDNA clones for KIAA genes: manual RT curation of 330 KIAA cDNA clones."; RL DNA Res. 9:99-106(2002). RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RX PubMed=15164053; DOI=10.1038/nature02465; RA Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., RA Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., RA Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., RA Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., RA Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., RA Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., RA Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., RA Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., RA Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., RA Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., RA Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., RA Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., RA Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., RA Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., RA Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., RA Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., RA Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., RA Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., RA McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., RA Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., RA Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., RA Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., RA Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., RA West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., RA Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., RA Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., RA Dunham I.; RT "DNA sequence and analysis of human chromosome 9."; RL Nature 429:369-374(2004). RN [5] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., RA Hunkapiller M.W., Myers E.W., Venter J.C.; RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases. RN [6] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2-1096. RC TISSUE=Amygdala; RX PubMed=17974005; DOI=10.1186/1471-2164-8-399; RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., RA Wiemann S., Schupp I.; RT "The full-ORF clone resource of the German cDNA consortium."; RL BMC Genomics 8:399-399(2007). RN [7] RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Cervix carcinoma; RX PubMed=17081983; DOI=10.1016/j.cell.2006.09.026; RA Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.; RT "Global, in vivo, and site-specific phosphorylation dynamics in signaling RT networks."; RL Cell 127:635-648(2006). RN [8] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-539 AND SER-882, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Cervix carcinoma; RX PubMed=18669648; DOI=10.1073/pnas.0805139105; RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., RA Elledge S.J., Gygi S.P.; RT "A quantitative atlas of mitotic phosphorylation."; RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008). RN [9] RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=19413330; DOI=10.1021/ac9004309; RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.; RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a RT refined SCX-based approach."; RL Anal. Chem. 81:4493-4501(2009). RN [10] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-882, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Leukemic T-cell; RX PubMed=19690332; DOI=10.1126/scisignal.2000007; RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., RA Rodionov V., Han D.K.; RT "Quantitative phosphoproteomic analysis of T cell receptor signaling RT reveals system-wide modulation of protein-protein interactions."; RL Sci. Signal. 2:RA46-RA46(2009). RN [11] RP SUBCELLULAR LOCATION. RX PubMed=20813266; DOI=10.1016/j.cell.2010.07.047; RA Ohta S., Bukowski-Wills J.C., Sanchez-Pulido L., Alves Fde L., Wood L., RA Chen Z.A., Platani M., Fischer L., Hudson D.F., Ponting C.P., Fukagawa T., RA Earnshaw W.C., Rappsilber J.; RT "The protein composition of mitotic chromosomes determined using RT multiclassifier combinatorial proteomics."; RL Cell 142:810-821(2010). RN [12] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-474; THR-479; SER-705 AND RP SER-882, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Cervix carcinoma; RX PubMed=20068231; DOI=10.1126/scisignal.2000475; RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.; RT "Quantitative phosphoproteomics reveals widespread full phosphorylation RT site occupancy during mitosis."; RL Sci. Signal. 3:RA3-RA3(2010). RN [13] RP FUNCTION, CATALYTIC ACTIVITY, PHOSPHORYLATION BY PKA, PHOSPHORYLATION AT RP SER-1056, INTERACTION WITH ARID5B; HNF4A AND NR1H4, IDENTIFICATION BY MASS RP SPECTROMETRY, TISSUE SPECIFICITY, IDENTIFICATION IN THE PHF2-ARID5B RP COMPLEX, AND MUTAGENESIS OF HIS-249; SER-757; SER-899; SER-954 AND RP SER-1056. RX PubMed=21532585; DOI=10.1038/ncb2228; RA Baba A., Ohtake F., Okuno Y., Yokota K., Okada M., Imai Y., Ni M., RA Meyer C.A., Igarashi K., Kanno J., Brown M., Kato S.; RT "PKA-dependent regulation of the histone lysine demethylase complex PHF2- RT ARID5B."; RL Nat. Cell Biol. 13:668-675(2011). RN [14] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-705, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=21406692; DOI=10.1126/scisignal.2001570; RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.; RT "System-wide temporal characterization of the proteome and phosphoproteome RT of human embryonic stem cell differentiation."; RL Sci. Signal. 4:RS3-RS3(2011). RN [15] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-539; SER-655; SER-705 AND RP SER-882, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Cervix carcinoma, and Erythroleukemia; RX PubMed=23186163; DOI=10.1021/pr300630k; RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J., RA Mohammed S.; RT "Toward a comprehensive characterization of a human cancer cell RT phosphoproteome."; RL J. Proteome Res. 12:260-271(2013). RN [16] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-474; SER-681; SER-882 AND RP SER-899, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Liver; RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014; RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., RA Ye M., Zou H.; RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver RT phosphoproteome."; RL J. Proteomics 96:253-262(2014). RN [17] RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-711, AND IDENTIFICATION BY MASS RP SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=28112733; DOI=10.1038/nsmb.3366; RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C., RA Nielsen M.L.; RT "Site-specific mapping of the human SUMO proteome reveals co-modification RT with phosphorylation."; RL Nat. Struct. Mol. Biol. 24:325-336(2017). RN [18] RP X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) OF 1-70 IN COMPLEX WITH ZINC, DOMAIN RP PHD-TYPE ZINC-FINGER, FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF RP TYR-7 AND TRP-29. RX PubMed=20129925; DOI=10.1074/jbc.c109.097667; RA Wen H., Li J., Song T., Lu M., Kan P.Y., Lee M.G., Sha B., Shi X.; RT "Recognition of histone H3K4 trimethylation by the plant homeodomain of RT PHF2 modulates histone demethylation."; RL J. Biol. Chem. 285:9322-9326(2010). RN [19] RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 60-451 IN COMPLEX WITH IRON AND RP N-OXALYLGLYCINE, FUNCTION, AND MUTAGENESIS OF TYR-321. RX PubMed=21167174; DOI=10.1016/j.jmb.2010.12.013; RA Horton J.R., Upadhyay A.K., Hashimoto H., Zhang X., Cheng X.; RT "Structural basis for human PHF2 Jumonji domain interaction with metal RT ions."; RL J. Mol. Biol. 406:1-8(2011). CC -!- FUNCTION: Lysine demethylase that demethylates both histones and non- CC histone proteins (PubMed:20129925, PubMed:21167174, PubMed:21532585). CC Enzymatically inactive by itself, and becomes active following CC phosphorylation by PKA: forms a complex with ARID5B and mediates CC demethylation of methylated ARID5B (PubMed:21532585). Demethylation of CC ARID5B leads to target the PHF2-ARID5B complex to target promoters, CC where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 CC (H3K9me2), followed by transcription activation of target genes CC (PubMed:21532585). The PHF2-ARID5B complex acts as a coactivator of CC HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone CC H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA CC (PubMed:21532585). Involved in the activation of toll-like receptor 4 CC (TLR4)-target inflammatory genes in macrophages by catalyzing the CC demethylation of trimethylated histone H4 lysine 20 (H4K20me3) at the CC gene promoters (By similarity). {ECO:0000250|UniProtKB:Q9WTU0, CC ECO:0000269|PubMed:20129925, ECO:0000269|PubMed:21167174, CC ECO:0000269|PubMed:21532585}. CC -!- CATALYTIC ACTIVITY: CC Reaction=2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + CC O2 = CO2 + formaldehyde + N(6)-methyl-L-lysyl(9)-[histone H3] + CC succinate; Xref=Rhea:RHEA:60192, Rhea:RHEA-COMP:15541, Rhea:RHEA- CC COMP:15542, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, CC ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:61929, CC ChEBI:CHEBI:61976; Evidence={ECO:0000269|PubMed:21532585}; CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60193; CC Evidence={ECO:0000269|PubMed:21532585}; CC -!- ACTIVITY REGULATION: Enzymatically inactive by itself, and become CC active following phosphorylation by PKA. CC -!- SUBUNIT: Component of the PHF2-ARID5B complex, at least composed of CC PHF2 and ARID5B (PubMed:21532585). Interacts with HNF4A and NR1H4 CC (PubMed:21532585). Interacts with RELA (By similarity). CC {ECO:0000250|UniProtKB:Q9WTU0, ECO:0000269|PubMed:21532585}. CC -!- INTERACTION: CC O75151; Q96RI1: NR1H4; NbExp=2; IntAct=EBI-10972034, EBI-1250177; CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:20129925}. CC Chromosome, centromere, kinetochore {ECO:0000269|PubMed:20813266}. CC -!- TISSUE SPECIFICITY: Widely expressed, including in liver (at protein CC level). {ECO:0000269|PubMed:21532585}. CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me2 and CC H3K4me3. {ECO:0000269|PubMed:20129925}. CC -!- PTM: Phosphorylated by PKA on specific serine residues, leading to the CC formation of an active lysine demethylase complex. CC {ECO:0000269|PubMed:21532585}. CC -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family. JHDM1D CC subfamily. {ECO:0000305}. CC -!- CAUTION: In contrast to the related histone demethylases JHDM1D and CC PHF8, the conserved active His in position 321 is replaced by a Tyr. CC However, the presence of a Tyr residue neither affects binding to the CC catalytic iron nor abolishes demethylase activity (PubMed:21167174). CC {ECO:0000305|PubMed:21167174}. CC -!- SEQUENCE CAUTION: CC Sequence=BAA31637.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AF043725; AAD21791.1; -; mRNA. DR EMBL; AB014562; BAA31637.2; ALT_INIT; mRNA. DR EMBL; AL353629; -; NOT_ANNOTATED_CDS; Genomic_DNA. DR EMBL; AL359181; -; NOT_ANNOTATED_CDS; Genomic_DNA. DR EMBL; CH471089; EAW62867.1; -; Genomic_DNA. DR EMBL; AL834263; CAD38938.1; -; mRNA. DR CCDS; CCDS35069.1; -. DR PIR; T00369; T00369. DR RefSeq; NP_005383.3; NM_005392.3. DR PDB; 3KQI; X-ray; 1.78 A; A=1-70. DR PDB; 3PTR; X-ray; 1.95 A; B=60-451. DR PDB; 3PU3; X-ray; 1.95 A; A/B=60-451. DR PDB; 3PU8; X-ray; 1.94 A; A/B=60-451. DR PDB; 3PUA; X-ray; 1.89 A; A=60-451. DR PDB; 3PUS; X-ray; 2.08 A; A/B=60-451. DR PDB; 7M10; X-ray; 1.15 A; A=1-70. DR PDB; 8F8Y; X-ray; 3.06 A; A/B=1-451. DR PDB; 8F8Z; X-ray; 3.30 A; A/B=1-451. DR PDBsum; 3KQI; -. DR PDBsum; 3PTR; -. DR PDBsum; 3PU3; -. DR PDBsum; 3PU8; -. DR PDBsum; 3PUA; -. DR PDBsum; 3PUS; -. DR PDBsum; 7M10; -. DR PDBsum; 8F8Y; -. DR PDBsum; 8F8Z; -. DR AlphaFoldDB; O75151; -. DR SMR; O75151; -. DR BioGRID; 111272; 60. DR ComplexPortal; CPX-7861; PHF2-ARID5B histone lysine demethylase complex. DR IntAct; O75151; 10. DR MINT; O75151; -. DR STRING; 9606.ENSP00000352185; -. DR BindingDB; O75151; -. DR ChEMBL; CHEMBL4295672; -. DR GlyGen; O75151; 1 site, 1 O-linked glycan (1 site). DR iPTMnet; O75151; -. DR PhosphoSitePlus; O75151; -. DR SwissPalm; O75151; -. DR BioMuta; PHF2; -. DR EPD; O75151; -. DR jPOST; O75151; -. DR MassIVE; O75151; -. DR MaxQB; O75151; -. DR PaxDb; 9606-ENSP00000352185; -. DR PeptideAtlas; O75151; -. DR ProteomicsDB; 49817; -. DR Pumba; O75151; -. DR Antibodypedia; 2009; 122 antibodies from 24 providers. DR DNASU; 5253; -. DR Ensembl; ENST00000359246.9; ENSP00000352185.4; ENSG00000197724.11. DR GeneID; 5253; -. DR KEGG; hsa:5253; -. DR MANE-Select; ENST00000359246.9; ENSP00000352185.4; NM_005392.4; NP_005383.3. DR UCSC; uc004aub.4; human. DR AGR; HGNC:8920; -. DR CTD; 5253; -. DR DisGeNET; 5253; -. DR GeneCards; PHF2; -. DR HGNC; HGNC:8920; PHF2. DR HPA; ENSG00000197724; Low tissue specificity. DR MIM; 604351; gene. DR neXtProt; NX_O75151; -. DR OpenTargets; ENSG00000197724; -. DR PharmGKB; PA33260; -. DR VEuPathDB; HostDB:ENSG00000197724; -. DR eggNOG; KOG1633; Eukaryota. DR GeneTree; ENSGT00940000158148; -. DR HOGENOM; CLU_003540_2_0_1; -. DR InParanoid; O75151; -. DR OMA; KDIVHTQ; -. DR OrthoDB; 2784357at2759; -. DR PhylomeDB; O75151; -. DR TreeFam; TF106480; -. DR BioCyc; MetaCyc:G66-32922-MONOMER; -. DR PathwayCommons; O75151; -. DR Reactome; R-HSA-3214842; HDMs demethylate histones. DR SignaLink; O75151; -. DR SIGNOR; O75151; -. DR BioGRID-ORCS; 5253; 39 hits in 1172 CRISPR screens. DR ChiTaRS; PHF2; human. DR EvolutionaryTrace; O75151; -. DR GenomeRNAi; 5253; -. DR Pharos; O75151; Tbio. DR PRO; PR:O75151; -. DR Proteomes; UP000005640; Chromosome 9. DR RNAct; O75151; Protein. DR Bgee; ENSG00000197724; Expressed in ganglionic eminence and 185 other cell types or tissues. DR ExpressionAtlas; O75151; baseline and differential. DR GO; GO:0000776; C:kinetochore; IDA:UniProtKB. DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB. DR GO; GO:0005654; C:nucleoplasm; IDA:HPA. DR GO; GO:0005634; C:nucleus; TAS:ProtInc. DR GO; GO:0032454; F:histone H3K9 demethylase activity; IDA:UniProtKB. DR GO; GO:0035575; F:histone H4K20 demethylase activity; ISS:UniProtKB. DR GO; GO:0005506; F:iron ion binding; IDA:UniProtKB. DR GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB. DR GO; GO:0003713; F:transcription coactivator activity; IDA:UniProtKB. DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central. DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB. DR GO; GO:0001889; P:liver development; TAS:UniProtKB. DR GO; GO:0061188; P:negative regulation of rDNA heterochromatin formation; IMP:UniProtKB. DR GO; GO:0006482; P:protein demethylation; IDA:UniProtKB. DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central. DR GO; GO:0045815; P:transcription initiation-coupled chromatin remodeling; ISS:UniProtKB. DR CDD; cd15554; PHD_PHF2_like; 1. DR Gene3D; 1.20.58.1360; -; 1. DR Gene3D; 2.60.120.650; Cupin; 1. DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1. DR InterPro; IPR041070; JHD. DR InterPro; IPR003347; JmjC_dom. DR InterPro; IPR019786; Zinc_finger_PHD-type_CS. DR InterPro; IPR011011; Znf_FYVE_PHD. DR InterPro; IPR001965; Znf_PHD. DR InterPro; IPR019787; Znf_PHD-finger. DR InterPro; IPR013083; Znf_RING/FYVE/PHD. DR PANTHER; PTHR23123:SF14; LYSINE-SPECIFIC DEMETHYLASE PHF2; 1. DR PANTHER; PTHR23123; PHD/F-BOX CONTAINING PROTEIN; 1. DR Pfam; PF17811; JHD; 1. DR Pfam; PF02373; JmjC; 1. DR Pfam; PF00628; PHD; 1. DR SMART; SM00558; JmjC; 1. DR SMART; SM00249; PHD; 1. DR SUPFAM; SSF51197; Clavaminate synthase-like; 1. DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 1. DR PROSITE; PS51184; JMJC; 1. DR PROSITE; PS01359; ZF_PHD_1; 1. DR PROSITE; PS50016; ZF_PHD_2; 1. DR Genevisible; O75151; HS. PE 1: Evidence at protein level; KW 3D-structure; Acetylation; Activator; Centromere; Chromatin regulator; KW Chromosome; Dioxygenase; Iron; Isopeptide bond; Kinetochore; Metal-binding; KW Nucleus; Oxidoreductase; Phosphoprotein; Reference proteome; Transcription; KW Transcription regulation; Ubl conjugation; Zinc; Zinc-finger. FT CHAIN 1..1096 FT /note="Lysine-specific demethylase PHF2" FT /id="PRO_0000059290" FT DOMAIN 197..353 FT /note="JmjC" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538" FT ZN_FING 5..56 FT /note="PHD-type" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146" FT REGION 447..634 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 646..674 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 719..799 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 817..846 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 877..1078 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 501..516 FT /note="Pro residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 518..536 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 551..565 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 581..628 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 725..753 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 776..799 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 885..902 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 959..1026 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 1052..1068 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 193 FT /ligand="2-oxoglutarate" FT /ligand_id="ChEBI:CHEBI:16810" FT BINDING 246 FT /ligand="2-oxoglutarate" FT /ligand_id="ChEBI:CHEBI:16810" FT BINDING 249 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538, FT ECO:0000269|PubMed:21167174" FT BINDING 251 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538, FT ECO:0000269|PubMed:21167174" FT BINDING 259 FT /ligand="2-oxoglutarate" FT /ligand_id="ChEBI:CHEBI:16810" FT BINDING 266 FT /ligand="2-oxoglutarate" FT /ligand_id="ChEBI:CHEBI:16810" FT BINDING 321 FT /ligand="2-oxoglutarate" FT /ligand_id="ChEBI:CHEBI:16810" FT BINDING 321 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538, FT ECO:0000269|PubMed:21167174" FT BINDING 323 FT /ligand="2-oxoglutarate" FT /ligand_id="ChEBI:CHEBI:16810" FT MOD_RES 474 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:20068231, FT ECO:0007744|PubMed:24275569" FT MOD_RES 479 FT /note="Phosphothreonine" FT /evidence="ECO:0007744|PubMed:20068231" FT MOD_RES 539 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:18669648, FT ECO:0007744|PubMed:23186163" FT MOD_RES 655 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:23186163" FT MOD_RES 681 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:24275569" FT MOD_RES 705 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:20068231, FT ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163" FT MOD_RES 720 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:Q9WTU0" FT MOD_RES 728 FT /note="Phosphotyrosine" FT /evidence="ECO:0000250|UniProtKB:Q9WTU0" FT MOD_RES 730 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q9WTU0" FT MOD_RES 733 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q9WTU0" FT MOD_RES 734 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q9WTU0" FT MOD_RES 738 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q9WTU0" FT MOD_RES 879 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q9WTU0" FT MOD_RES 882 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:18669648, FT ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, FT ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569" FT MOD_RES 899 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:24275569" FT MOD_RES 1056 FT /note="Phosphoserine; by PKA" FT /evidence="ECO:0000269|PubMed:21532585" FT CROSSLNK 711 FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with FT G-Cter in SUMO2)" FT /evidence="ECO:0007744|PubMed:28112733" FT VARIANT 56 FT /note="T -> P (in dbSNP:rs34279404)" FT /id="VAR_047553" FT VARIANT 1058 FT /note="S -> L (in dbSNP:rs35236745)" FT /id="VAR_051598" FT MUTAGEN 7 FT /note="Y->A: Abolishes binding to H3K4me2 and H3K4me3." FT /evidence="ECO:0000269|PubMed:20129925" FT MUTAGEN 29 FT /note="W->A: Abolishes binding to H3K4me2 and H3K4me3." FT /evidence="ECO:0000269|PubMed:20129925" FT MUTAGEN 249 FT /note="H->A: Abolishes demethylase activity." FT /evidence="ECO:0000269|PubMed:21532585" FT MUTAGEN 321 FT /note="Y->H: Does not alter iron-binding nor activates FT histone demethylase activity." FT /evidence="ECO:0000269|PubMed:21167174" FT MUTAGEN 757 FT /note="S->A: Abolishes phosphorylation by PKA and FT activation of demethylase activity; when associated with FT A-899; A-954 and A-1056." FT /evidence="ECO:0000269|PubMed:21532585" FT MUTAGEN 899 FT /note="S->A: Abolishes phosphorylation by PKA and FT activation of demethylase activity; when associated with FT A-757; A-954 and A-1056." FT /evidence="ECO:0000269|PubMed:21532585" FT MUTAGEN 954 FT /note="S->A: Abolishes phosphorylation by PKA and FT activation of demethylase activity; when associated with FT A-757; A-899 and A-1056." FT /evidence="ECO:0000269|PubMed:21532585" FT MUTAGEN 1056 FT /note="S->A: Abolishes phosphorylation by PKA and FT activation of demethylase activity; when associated with FT A-757; A-899 and A-954." FT /evidence="ECO:0000269|PubMed:21532585" FT CONFLICT 19..41 FT /note="FMIECDACKDWFHGSCVGVEEEE -> PRAARPPARPGPTRAAQRRGRAT FT (in Ref. 2; BAA31637)" FT /evidence="ECO:0000305" FT CONFLICT 75..76 FT /note="QA -> PT (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 100 FT /note="S -> R (in Ref. 2; BAA31637)" FT /evidence="ECO:0000305" FT CONFLICT 106 FT /note="A -> S (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 115 FT /note="L -> V (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 621 FT /note="K -> R (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 633 FT /note="Missing (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 642 FT /note="K -> R (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 654 FT /note="T -> S (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 664 FT /note="N -> S (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 670 FT /note="P -> A (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 698 FT /note="N -> S (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 712..719 FT /note="AVLPTPVT -> EALLMPTS (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 727 FT /note="A -> V (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 752 FT /note="R -> K (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 782 FT /note="S -> N (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 817 FT /note="A -> T (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 823 FT /note="S -> G (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 833 FT /note="N -> I (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 837..841 FT /note="SGKSA -> NKGT (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 849 FT /note="A -> T (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 857 FT /note="D -> E (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 862 FT /note="Missing (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 888 FT /note="I -> V (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 949..950 FT /note="SK -> NR (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 954..955 FT /note="SA -> NT (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 959..960 FT /note="LT -> PA (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 964 FT /note="T -> A (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 968 FT /note="T -> I (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 972 FT /note="I -> ASASTGTT (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 975 FT /note="G -> S (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 978..979 FT /note="ST -> PA (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 996 FT /note="T -> TTPAST (in Ref. 2; BAA31637 and 6; CAD38938)" FT /evidence="ECO:0000305" FT CONFLICT 1033..1035 FT /note="TGA -> SGS (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 1040 FT /note="T -> A (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT CONFLICT 1063 FT /note="Missing (in Ref. 1; AAD21791)" FT /evidence="ECO:0000305" FT STRAND 2..5 FT /evidence="ECO:0007829|PDB:8F8Y" FT TURN 8..11 FT /evidence="ECO:0007829|PDB:7M10" FT STRAND 20..22 FT /evidence="ECO:0007829|PDB:7M10" FT TURN 24..26 FT /evidence="ECO:0007829|PDB:7M10" FT STRAND 29..31 FT /evidence="ECO:0007829|PDB:7M10" FT HELIX 32..35 FT /evidence="ECO:0007829|PDB:7M10" FT HELIX 39..44 FT /evidence="ECO:0007829|PDB:7M10" FT STRAND 45..47 FT /evidence="ECO:0007829|PDB:7M10" FT HELIX 51..57 FT /evidence="ECO:0007829|PDB:7M10" FT HELIX 87..95 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 101..103 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 105..107 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 110..112 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 115..121 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 127..131 FT /evidence="ECO:0007829|PDB:3PUA" FT TURN 133..136 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 146..153 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 158..163 FT /evidence="ECO:0007829|PDB:3PUA" FT TURN 164..166 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 169..173 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 174..181 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 183..185 FT /evidence="ECO:0007829|PDB:8F8Y" FT STRAND 190..196 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 201..205 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 210..215 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 217..221 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 236..240 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 245..249 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 252..254 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 256..271 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 275..286 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 290..292 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 295..298 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 303..308 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 312..315 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 320..336 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 339..341 FT /evidence="ECO:0007829|PDB:3PU8" FT HELIX 342..355 FT /evidence="ECO:0007829|PDB:3PUA" FT STRAND 359..361 FT /evidence="ECO:0007829|PDB:3PU3" FT HELIX 366..387 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 393..409 FT /evidence="ECO:0007829|PDB:3PUA" FT TURN 412..414 FT /evidence="ECO:0007829|PDB:3PU8" FT HELIX 415..418 FT /evidence="ECO:0007829|PDB:3PU8" FT HELIX 419..421 FT /evidence="ECO:0007829|PDB:3PUA" FT HELIX 428..443 FT /evidence="ECO:0007829|PDB:3PUA" SQ SEQUENCE 1096 AA; 120775 MW; DD088363DB76674D CRC64; MATVPVYCVC RLPYDVTRFM IECDACKDWF HGSCVGVEEE EAPDIDIYHC PNCEKTHGKS TLKKKRTWHK HGPGQAPDVK PVQNGSQLFI KELRSRTFPS AEDVVARVPG SQLTLGYMEE HGFTEPILVP KKDGLGLAVP APTFYVSDVE NYVGPERSVD VTDVTKQKDC KMKLKEFVDY YYSTNRKRVL NVTNLEFSDT RMSSFVEPPD IVKKLSWVEN YWPDDALLAK PKVTKYCLIC VKDSYTDFHI DSGGASAWYH VLKGEKTFYL IRPASANISL YERWRSASNH SEMFFADQVD KCYKCIVKQG QTLFIPSGWI YATLTPVDCL AFAGHFLHSL SVEMQMRAYE VERRLKLGSL TQFPNFETAC WYMGKHLLEA FKGSHKSGKQ LPPHLVQGAK ILNGAFRSWT KKQALAEHED ELPEHFKPSQ LIKDLAKEIR LSENASKAVR PEVNTVASSD EVCDGDREKE EPPSPIEATP PQSLLEKVSK KKTPKTVKMP KPSKIPKPPK PPKPPRPPKT LKLKDGGKKK GKKSRESASP TIPNLDLLEA HTKEALTKME PPKKGKATKS VLSVPNKDVV HMQNDVERLE IREQTKSKSE AKWKYKNSKP DSLLKMEEEQ KLEKSPLAGN KDNKFSFSFS NKKLLGSKAL RPPTSPGVFG ALQNFKEDKP KPVRDEYEYV SDDGELKIDE FPIRRKKNAP KRDLSFLLDK KAVLPTPVTK PKLDSAAYKS DDSSDEGSLH IDTDTKPGRN ARVKKESGSS AAGILDLLQA SEEVGALEYN PSSQPPASPS TQEAIQGMLS MANLQASDSC LQTTWGAGQA KGSSLAAHGA RKNGGGSGKS AGKRLLKRAA KNSVDLDDYE EEQDHLDACF KDSDYVYPSL ESDEDNPIFK SRSKKRKGSD DAPYSPTARV GPSVPRQDRP VREGTRVASI ETGLAAAAAK LSQQEEQKSK KKKSAKRKLT PNTTSPSTST SISAGTTSTS TTPASTTPAS TTPASTSTAS SQASQEGSSP EPPPESHSSS LADHEYTAAG TFTGAQAGRT SQPMAPGVFL TQRRPSASSP NNNTAAKGKR TKKGMATAKQ RLGKILKIHR NGKLLL //