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Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases

Nature Structural & Molecular Biology volume 17, pages 3843 (2010) | Download Citation

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Abstract

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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Acknowledgements

We thank A. Ruiz and R. Gridds for technical assistance, R.M. Blumenthal for critical comments, A.S. Bhagwat and T.W. Roy (Wayne State University) for Escherichia coli strain BH249 overexpressing formaldehyde dehydrogenase and T. Kutateladze (University of Colorado) and A. Mattevi and C. Binda (University of Pavia) for H3K4me3-containing peptides. The Department of Biochemistry at the Emory University School of Medicine supported the use of the SER-CAT synchrotron beamline at the Advanced Photon Source of Argonne National Laboratory, local X-ray facility and MALDI-TOF mass spectrometry. This work was supported by grants GM06860 and DK082678 to X.C. and GM058012 and NCI118487 to Y.S. from the US National Institutes of Health. Y.S. is a cofounder of Constellation Pharmaceutical. X.C. is a Georgia Research Alliance Eminent Scholar.

Author information

Author notes

    • John R Horton
    • , Anup K Upadhyay
    •  & Hank H Qi

    These authors contributed equally to this work.

Affiliations

  1. Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.

    • John R Horton
    • , Anup K Upadhyay
    • , Xing Zhang
    •  & Xiaodong Cheng
  2. Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.

    • Hank H Qi
    •  & Yang Shi
  3. Division of Newborn Medicine, Department of Medicine, Children's Hospital, Boston, Massachusetts, USA.

    • Hank H Qi
    •  & Yang Shi

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Contributions

J.R.H. performed crystallographic experiments; A.K.U. performed kinetic experiments; H.H.Q. and Y.S. provided initial expression constructs and the knowledge of specificities of individual PHD and jumonji domains; X.Z. generated hybrid enzymes; X.C. organized and designed the scope of the study and wrote the manuscript, and all others helped in analyzing data and revising the manuscript.

Corresponding author

Correspondence to Xiaodong Cheng.

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https://doi.org/10.1038/nsmb.1753

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