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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).
Bannister, A.J., Schneider, R. & Kouzarides, T. Histone methylation: dynamic or static? Cell 109, 801–806 (2002).
Shi, Y. & Whetstine, J.R. Dynamic regulation of histone lysine methylation by demethylases. Mol. Cell 25, 1–14 (2007).
Shi, Y. et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941–953 (2004).
Metzger, E. et al. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437, 436–439 (2005).
Tsukada, Y. et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439, 811–816 (2006).
Clifton, I.J. et al. Structural studies on 2-oxoglutarate oxygenases and related double-stranded beta-helix fold proteins. J. Inorg. Biochem. 100, 644–669 (2006).
Schneider, J. & Shilatifard, A. Histone demethylation by hydroxylation: chemistry in action. ACS Chem. Biol. 1, 75–81 (2006).
Klose, R.J. et al. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442, 312–316 (2006).
Yamane, K. et al. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125, 483–495 (2006).
Cloos, P.A. et al. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442, 307–311 (2006).
Fodor, B.D. et al. Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev. 20, 1557–1562 (2006).
Shin, S. & Janknecht, R. Diversity within the JMJD2 histone demethylase family. Biochem. Biophys. Res. Commun. 353, 973–977 (2007).
Whetstine, J.R. et al. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125, 467–481 (2006).
Secombe, J., Li, L., Carlos, L. & Eisenman, R.N. The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth. Genes Dev. 21, 537–551 (2007).
Klose, R.J. et al. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128, 889–900 (2007).
Lee, M.G., Norman, J., Shilatifard, A. & Shiekhattar, R. Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a Polycomb-like protein. Cell 128, 877–887 (2007).
Seward, D.J. et al. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat. Struct. Mol. Biol. 14, 240–242 (2007).
Iwase, S. et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128, 1077–1088 (2007).
Eissenberg, J.C. et al. The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat. Struct. Mol. Biol. 14, 344–346 (2007).
Christensen, J. et al. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128, 1063–1076 (2007).
Lee, N. et al. The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase. Nat. Struct. Mol. Biol. 14, 341–343 (2007).
Liang, G., Klose, R.J., Gardner, K.E. & Zhang, Y. Yeast Jhd2p is a histone H3 Lys4 trimethyl demethylase. Nat. Struct. Mol. Biol. 14, 243–245 (2007).
Klose, R.J. et al. Demethylation of histone H3K36 and H3K9 by Rph1: a vestige of an H3K9 methylation system in Saccharomyces cerevisiae? Mol. Cell. Biol. 27, 3951–3961 (2007).
Katoh, M. Identification and characterization of JMJD2 family genes in silico. Int. J. Oncol. 24, 1623–1628 (2004).
Wissmann, M. et al. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat. Cell Biol. 9, 347–353 (2007).
Chen, Z. et al. Structural insights into histone demethylation by JMJD2 family members. Cell 125, 691–702 (2006).
Trievel, R.C., Flynn, E.M., Houtz, R.L. & Hurley, J.H. Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT. Nat. Struct. Biol. 10, 545–552 (2003).
Couture, J.F., Hauk, G., Thompson, M.J., Blackburn, G.M. & Trievel, R.C. Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases. J. Biol. Chem. 281, 19280–19287 (2006).
Derewenda, Z.S., Lee, L. & Derewenda, U. The occurrence of C-H···O hydrogen bonds in proteins. J. Mol. Biol. 252, 248–262 (1995).
Fischle, W. et al. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17, 1870–1881 (2003).
Huang, Y., Fang, J., Bedford, M.T., Zhang, Y. & Xu, R.M. Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science 312, 748–751 (2006).
Botuyan, M.V. et al. Structural basis for the methylation state-specific recognition of histone H4–K20 by 53BP1 and Crb2 in DNA repair. Cell 127, 1361–1373 (2006).
Li, H. et al. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442, 91–95 (2006).
Pena, P.V. et al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442, 100–103 (2006).
Kim, J. et al. Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Rep. 7, 397–403 (2006).
Jacobs, S.A. & Khorasanizadeh, S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295, 2080–2083 (2002).
Nielsen, P.R. et al. Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416, 103–107 (2002).
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
Messerschmidt, A. & Pflugrath, J.W. Crystal orientation and X-ray pattern prediction routines for area-detector diffractometer systems in macromolecular crystallography. J. Appl. Cryst. 20, 306–315 (1987).
Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022–1025 (1997).
Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).
Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).
Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 24, 946–950 (1993).
Lee, B. & Richards, F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400 (1971).
Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991).
Guex, N. & Peitsch, M.C. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18, 2714–2723 (1997).
Lizcano, J.M., Unzeta, M. & Tipton, K.F. A spectrophotometric method for determining the oxidative deamination of methylamine by the amine oxidases. Anal. Biochem. 286, 75–79 (2000).
Kerr, R.G. & Kelly, K. An enzyme-based formaldehyde assay and its utility in a sponge sterol biosynthetic pathway. J. Nat. Prod. 62, 201–202 (1999).
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.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Fig. 1
Sequence alignment of the catalytic domains of trimethyllysine-specific JmjC HDMs. (PDF 141 kb)
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nsmb1273
This article is cited by
-
Chromatin balances cell redox and energy homeostasis
Epigenetics & Chromatin (2023)
-
In-silico guided chemical exploration of KDM4A fragments hits
Clinical Epigenetics (2023)
-
KDM4A, involved in the inflammatory and oxidative stress caused by traumatic brain injury-hemorrhagic shock, partly through the regulation of the microglia M1 polarization
BMC Neuroscience (2023)
-
Carcinogenesis promotion in oral squamous cell carcinoma: KDM4A complex-mediated gene transcriptional suppression by LEF1
Cell Death & Disease (2023)
-
JMJD family proteins in cancer and inflammation
Signal Transduction and Targeted Therapy (2022)