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Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases
Open accessAbstract
Combinatorial readout of multiple covalent histone modifications is poorly understood. We provide insights into how an activating histone mark, in combination with linked repressive marks, is differentially 'read' by two related human demethylases, PHF8 and KIAA1718 (also known as JHDM1D). Both enzymes harbor a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. The presence of H3K4me3 on the same peptide as H3K9me2 makes the doubly methylated peptide a markedly better substrate of PHF8, whereas the presence of H3K4me3 has the opposite effect, diminishing the H3K9me2 demethylase activity of KIAA1718 without adversely affecting its H3K27me2 activity. The difference in substrate specificity between the two is explained by PHF8 adopting a bent conformation, allowing each of its domains to engage its respective target, whereas KIAA1718 adopts an extended conformation, which prevents its access to H3K9me2 by its jumonji domain when its PHD engages H3K4me3.
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“KDM7A (encoding Lysine Demethylase 7A), which plays a central role in the nervous system and midbrain development (Horton et al., 2010; Qi et al., 2010; Tsukada et al., 2010).”
From Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders (2019) · cites this paper as Horton et al., 2010
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Histone methylation: a dynamic mark in health, disease and inheritance
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Metadata
- Authors
- Horton, J. R., Upadhyay, A. K., Qi, H. H., Zhang, X., Shi, Y., & Cheng, X.
- Affiliations
- Emory University (US)
- Boston Children's Hospital (US)
- Corresponding author
- Cheng, Xiaodong
- Venue
- Nature Structural & Molecular Biology
- Published
- 2009-12-20
- Volume
- 17
- Issue
- 1
- Pages
- 38-43
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC2849977
- OpenAlex
- W2132614547
- Cited by
- 389
- References
- 46
- Citations by year
- 2026: 10 · 2025: 14 · 2024: 22 · 2023: 12 · 2022: 13 · 2021: 24 · 2020: 22 · 2019: 27 · 2018: 18 · 2017: 19 · 2016: 30 · 2015: 27 · 2014: 27 · 2013: 28 · 2012: 26
- FWCI
- 12.25
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Public Health Service (NCI118487)
- National Institute of General Medical Sciences (GM058012, R01GM058012, R01GM068680, GM06860)
- National Institute of Diabetes and Digestive and Kidney Diseases (R56DK082678, DK082678)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
- Keywords
- PHF8, plant homeodomain, histone lysine demethylation, H3K4me3, H3K9me2, H3K27me2, substrate specificity, protein conformation, histone modifications, transcriptional activation, histone reader proteins
- MeSH terms
- Histones, Humans, Models, Molecular, Oxidoreductases, N-Demethylating, Protein Binding, Protein Conformation, Substrate Specificity, Transcription Factors, Protein Structure, Tertiary, F-Box Proteins, Histone Demethylases, Jumonji Domain-Containing Histone Demethylases
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