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- SASDFU3: Lysine-specific Demethylase (LSD2) (Lysyne-specific Demethylase L... -

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Basic information

Entry
Database: SASBDB / ID: SASDFU3
SampleLysine-specific Demethylase (LSD2)
  • Lysyne-specific Demethylase LSD2 (protein), LSD2, Homo sapiens
Function / homology
Function and homology information


epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / transcription initiation-coupled chromatin remodeling / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding / HDMs demethylate histones / UCH proteinases ...epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / transcription initiation-coupled chromatin remodeling / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding / HDMs demethylate histones / UCH proteinases / nucleosome / flavin adenine dinucleotide binding / histone binding / oxidoreductase activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationJournal: Cell Rep / Year: 2019
Title: A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
Authors: Chiara Marabelli / Biagina Marrocco / Simona Pilotto / Sagar Chittori / Sarah Picaud / Sara Marchese / Giuseppe Ciossani / Federico Forneris / Panagis Filippakopoulos / Guy Schoehn / Daniela ...Authors: Chiara Marabelli / Biagina Marrocco / Simona Pilotto / Sagar Chittori / Sarah Picaud / Sara Marchese / Giuseppe Ciossani / Federico Forneris / Panagis Filippakopoulos / Guy Schoehn / Daniela Rhodes / Sriram Subramaniam / Andrea Mattevi /
Abstract: LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase ...LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide from the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.
Contact author
  • Federico Forneris (University of Pavia)

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Structure visualization

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Models

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Sample

SampleName: Lysine-specific Demethylase (LSD2) / Specimen concentration: 2 mg/ml
BufferName: 15 mM HEPES, 200 mM NaCl / pH: 7.3
Entity #1516Name: LSD2 / Type: protein / Description: Lysyne-specific Demethylase LSD2 / Formula weight: 88.832 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q8NB78
Sequence: KKKATETTDE DEDGGSEKKY RKCEKAGCTA TCPVCFASAS ERCAKNGYTS RWYHLSCGEH FCNECFDHYY RSHKDGYDKY TTWKKIWTSN GKTEPSPKAF MADQQLPYWV QCTKPECRKW RQLTKEIQLT PQIAKTYRCG MKPNTAIKPE TSDHCSLPED LRVLEVSNHW ...Sequence:
KKKATETTDE DEDGGSEKKY RKCEKAGCTA TCPVCFASAS ERCAKNGYTS RWYHLSCGEH FCNECFDHYY RSHKDGYDKY TTWKKIWTSN GKTEPSPKAF MADQQLPYWV QCTKPECRKW RQLTKEIQLT PQIAKTYRCG MKPNTAIKPE TSDHCSLPED LRVLEVSNHW WYSMLILPPL LKDSVAAPLL SAYYPDCVGM SPSCTSTNRA AATGNASPGK LEHSKAALSV HVPGMNRYFQ PFYQPNECGK ALCVRPDVME LDELYEFPEY SRDPTMYLAL RNLILALWYT NCKEALTPQK CIPHIIVRGL VRIRCVQEVE RILYFMTRKG LINTGVLSVG ADQYLLPKDY HNKSVIIIGA GPAGLAAARQ LHNFGIKVTV LEAKDRIGGR VWDDKSFKGV TVGRGAQIVN GCINNPVALM CEQLGISMHK FGERCDLIQE GGRITDPTID KRMDFHFNAL LDVVSEWRKD KTQLQDVPLG EKIEEIYKAF IKESGIQFSE LEGQVLQFHL SNLEYACGSN LHQVSARSWD HNEFFAQFAG DHTLLTPGYS VIIEKLAEGL DIQLKSPVQC IDYSGDEVQV TTTDGTGYSA QKVLVTVPLA LLQKGAIQFN PPLSEKKMKA INSLGAGIIE KIALQFPYRF WDSKVQGADF FGHVPPSASK RGLFAVFYDM DPQKKHSVLM SVIAGEAVAS VRTLDDKQVL QQCMATLREL FKEQEVPDPT KYFVTRWSTD PWIQMAYSFV KTGGSGEAYD IIAEDIQGTV FFAGEATNRH FPQTVTGAYL SGVREASKIA AF

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Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 2.87 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Lysine-specific Demethylase (LSD2) / Measurement date: Dec 11, 2017 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 167 / Unit: 1/nm /
MinMax
Q0.0573 2.8524
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 485 /
MinMax
Q0.104269 2.37796
P(R) point1 485
R0 10.59
Result
Type of curve: sec /
ExperimentalPorod
MW89.8 kDa78 kDa
Volume-124 nm3

P(R)GuinierGuinier error
Forward scattering, I027.01 26.89 0.1
Radius of gyration, Rg3.405 nm3.36 nm0.01

MinMax
D-10.59
Guinier point15 74

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