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- SASDFV3: Cytokine-like nuclear factor dehydrogenase domain, NPAC DH (NPAC ... -

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Basic information

Entry
Database: SASBDB / ID: SASDFV3
SampleCytokine-like nuclear factor dehydrogenase domain, NPAC DH (NPAC delta-261)
  • NPAC dehydrogenase domain (protein), NPAC DH, Homo sapiens
Function / homology
Function and homology information


chromatin-protein adaptor activity / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription initiation-coupled chromatin remodeling / methylated histone binding / NAD binding / nucleosome / NADP binding / histone binding / oxidoreductase activity ...chromatin-protein adaptor activity / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription initiation-coupled chromatin remodeling / methylated histone binding / NAD binding / nucleosome / NADP binding / histone binding / oxidoreductase activity / chromatin binding / chromatin / DNA binding / nucleoplasm / cytosol
Similarity search - Function
NP60, PWWP domain / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. ...NP60, PWWP domain / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Cytokine-like nuclear factor N-PAC
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: Cytokine-like nuclear factor dehydrogenase domain, NPAC DH (NPAC delta-261)
Specimen concentration: 1.5 mg/ml
BufferName: 15 mM HEPES, 200 mM NaCl / pH: 7.3
Entity #1518Name: NPAC DH / Type: protein / Description: NPAC dehydrogenase domain / Formula weight: 31.369 / Num. of mol.: 4 / Source: Homo sapiens / References: UniProt: Q49A26
Sequence: GSITPTDKKI GFLGLGLMGS GIVSNLLKMG HTVTVWNRTA EKCDLFIQEG ARLGRTPAEV VSTCDITFAC VSDPKAAKDL VLGPSGVLQG IRPGKCYVDM STVDADTVTE LAQVIVSRGG RFLEAPVSGN QQLSNDGMLV ILAAGDRGLY EDCSSCFQAM GKTSFFLGEV ...Sequence:
GSITPTDKKI GFLGLGLMGS GIVSNLLKMG HTVTVWNRTA EKCDLFIQEG ARLGRTPAEV VSTCDITFAC VSDPKAAKDL VLGPSGVLQG IRPGKCYVDM STVDADTVTE LAQVIVSRGG RFLEAPVSGN QQLSNDGMLV ILAAGDRGLY EDCSSCFQAM GKTSFFLGEV GNAAKMMLIV NMVQGSFMAT IAEGLTLAQV TGQSQQTLLD ILNQGQLASI FLDQKCQNIL QGNFKPDFYL KYIQKDLRLA IALGDAVNHP TPMAAAANEV YKRAKALDQS DNDMSAVYRA YIH

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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: Cytokine-like nuclear factor dehydrogenase domain, NPAC DH (NPAC delta-261)
Measurement date: Jan 26, 2018 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 173 / Unit: 1/nm /
MinMax
Q0.0748 2.8486
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 463 /
MinMax
Q0.102962 2.27128
P(R) point1 463
R0 10.96
Result
Type of curve: sec /
ExperimentalPorod
MW125 kDa104 kDa
Volume-167 nm3

P(R)GuinierGuinier error
Forward scattering, I014.08 14.04 0.036
Radius of gyration, Rg3.538 nm3.53 nm0.01

MinMax
D-10.96
Guinier point15 71

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