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- PDB-8e4v: Solution structure of the WH domain of MORF -

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Entry
Database: PDB / ID: 8e4v
TitleSolution structure of the WH domain of MORF
ComponentsIsoform 3 of Histone acetyltransferase KAT6B
KeywordsTRANSCRIPTION / MORF / winged helix / DNA / histone / chromatin
Function / homology
Function and homology information


histone H3 acetyltransferase activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / protein-lysine-acetyltransferase activity / histone acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity ...histone H3 acetyltransferase activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / protein-lysine-acetyltransferase activity / histone acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / transcription coregulator activity / nucleosome / nucleosome assembly / HATs acetylate histones / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 ...: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone acetyltransferase KAT6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, Y. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2023
Title: MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain.
Authors: Dustin C Becht / Brianna J Klein / Akinori Kanai / Suk Min Jang / Khan L Cox / Bing-Rui Zhou / Sabrina K Phanor / Yi Zhang / Ruo-Wen Chen / Christopher C Ebmeier / Catherine Lachance / ...Authors: Dustin C Becht / Brianna J Klein / Akinori Kanai / Suk Min Jang / Khan L Cox / Bing-Rui Zhou / Sabrina K Phanor / Yi Zhang / Ruo-Wen Chen / Christopher C Ebmeier / Catherine Lachance / Maxime Galloy / Amelie Fradet-Turcotte / Martha L Bulyk / Yawen Bai / Michael G Poirier / Jacques Côté / Akihiko Yokoyama / Tatiana G Kutateladze /
Abstract: Human acetyltransferases MOZ and MORF are implicated in chromosomal translocations associated with aggressive leukemias. Oncogenic translocations involve the far amino terminus of MOZ/MORF, the ...Human acetyltransferases MOZ and MORF are implicated in chromosomal translocations associated with aggressive leukemias. Oncogenic translocations involve the far amino terminus of MOZ/MORF, the function of which remains unclear. Here, we identified and characterized two structured winged helix (WH) domains, WH1 and WH2, in MORF and MOZ. WHs bind DNA in a cooperative manner, with WH1 specifically recognizing unmethylated CpG sequences. Structural and genomic analyses show that the DNA binding function of WHs targets MORF/MOZ to gene promoters, stimulating transcription and H3K23 acetylation, and WH1 recruits oncogenic fusions to HOXA genes that trigger leukemogenesis. Cryo-EM, NMR, mass spectrometry and mutagenesis studies provide mechanistic insight into the DNA-binding mechanism, which includes the association of WH1 with the CpG-containing linker DNA and binding of WH2 to the dyad of the nucleosome. The discovery of WHs in MORF and MOZ and their DNA binding functions could open an avenue in developing therapeutics to treat diseases associated with aberrant MOZ/MORF acetyltransferase activities.
History
DepositionAug 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Histone acetyltransferase KAT6B


Theoretical massNumber of molelcules
Total (without water)9,5161
Polymers9,5161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Isoform 3 of Histone acetyltransferase KAT6B / Histone acetyltransferase MOZ2 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 4 / MYST-4 / Monocytic ...Histone acetyltransferase MOZ2 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 4 / MYST-4 / Monocytic leukemia zinc finger protein-related factor


Mass: 9515.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6B, KIAA0383, MORF, MOZ2, MYST4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WYB5, histone acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D (H)CCH-TOCSY
161isotropic23D 1H-13C NOESY
171isotropic23D 1H-15N NOESY
181isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution / Contents: 1.33 mM [U-13C; U-15N] MORF-WH, 90% H2O/10% D2O / Label: 13C/15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.33 mM / Component: MORF-WH / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.8 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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