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Publication Abstract from PubMed

Saccharomyces cerevesiae Rph1 is a histone demethylase orthologous to human JMJD2A that can specifically demethylate tri- and dimethylated Lys36 of histone H3. The catalytic core of Rph1 (c-Rph1) is responsible for the demethylase activity which is essential for the transcription elongation of some actively transcribed genes. We report here the crystal structures of c-Rph1 in apo form and in complex with Ni2+ and alpha-ketoglutarate (alpha-KG). The structure of c-Rph1 is composed of a JmjN domain, a long beta-hairpin, a mixed structural motif, and a JmjC domain. The alpha-KG co-factor forms hydrogen-bonding interactions with the side chains of conserved residues, and the Ni2+ ion at the active site is chelated by conserved residues and the cofactor. Structural comparison of Rph1 with JMJD2A indicates that the substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin, and the mixed structural motif; and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. In vitro biochemical data show that mutations of the key residues at the catalytic center and in the substrate-binding cleft abolish the demethylase activity. In vivo growth phenotype analyses also demonstrate that these residues are essential for its functional roles in transcription elongation. Taken together, our structural and biological data provide insights into the molecular basis of the histone demethylase activity and the substrate specificity of Rph1.

Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.,Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J Biochem J. 2010 Nov 10. PMID:21067515^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.