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Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase

Nature Structural & Molecular Biology volume 14, pages 689–695 (2007)Cite this article

Abstract

JMJD2A is a JmjC histone demethylase (HDM) that catalyzes the demethylation of di- and trimethylated Lys9 and Lys36 in histone H3 (H3K9me2/3 and H3K36me2/3). Here we present the crystal structures of the JMJD2A catalytic domain in complex with H3K9me3, H3K36me2 and H3K36me3 peptides. The structures reveal that histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated ε-ammonium cation is coordinated within a methylammonium-binding pocket through carbon-oxygen (CH···O) hydrogen bonds that position one of the ζ-methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation. Mutations of the residues comprising this pocket abrogate demethylation by JMJD2A, with the exception of an S288A substitution, which augments activity, particularly toward H3K9me2. We propose that this residue modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs.

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Figure 1: Crystal structures of JMJD2A ternary complexes.
Figure 2: Histone substrate specificity of JMJD2A.
Figure 3: Methyllysine binding by JMJD2A.

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Acknowledgements

We thank D. Engelke for reading the manuscript and furnishing useful comments, P.J. O'Brien for advice regarding protein expression and J. Leykam at the Michigan State University Macromolecular Structure, Sequencing and Synthesis Facility for his assistance with amino acid analysis. Use of the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract no. W-31-109-ENG-38. The GM/CA CAT has been funded in whole or in part with Federal funds from the National Cancer Institute (Y1-CO-1020) and the National Institute of General Medical Science (Y1-GM-1104) of the US National Institutes of Health (NIH), and we thank R. Sanishvili, D. Yoder and S. Corcoran for their assistance with data collection at beamline ID-23. Use of the University of Michigan DNA Sequencing Core was supported by the NIH through the University of Michigan's Cancer Center Support Grant (5 P30 CA46592). J.-F.C. is a Canadian Institutes of Health Sciences postdoctoral fellow. This work was supported by grants from the University of Michigan's Office of the Vice President for Research and from the NIH (GM073839) to R.C.T.

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  1. Jean-François Couture and Evys Collazo: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, 48109-0606, Michigan, USA

    Jean-François Couture, Evys Collazo, Patricia A Ortiz-Tello & Raymond C Trievel

  2. Northwestern University Center for Synchrotron Research, Life Sciences Collaborative Access Team, Argonne, 60439, Illinois, USA

    Joseph S Brunzelle

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  1. Jean-François Couture
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Correspondence to Raymond C Trievel.

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Supplementary information

Supplementary Fig. 1

Sequence alignment of the catalytic domains of trimethyllysine-specific JmjC HDMs. (PDF 141 kb)

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Couture, JF., Collazo, E., Ortiz-Tello, P. et al. Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase. Nat Struct Mol Biol 14, 689–695 (2007). https://doi.org/10.1038/nsmb1273

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