Ribosomal oxygenases are structurally conserved from prokaryotes to humans

Abstract

2-Oxoglutarate (2OG)-dependent oxygenases play important roles in the regulation of gene expression via demethylation of N-methylated chromatin components1,2, hydroxylation of transcription factors3, and of splicing factor proteins4. Recently, 2OG-oxygenases that catalyze hydroxylation of tRNA5-7 and ribosomal proteins8, have been shown to play roles in translation relating to cellular growth, TH17-cell differentiation and translational accuracy9-12. The finding that the ribosomal oxygenases (ROX) occur in organisms ranging from prokaryotes to humans8 raises questions as to their structural and evolutionary relationships. In Escherichia coli, ycfD catalyzes arginine-hydroxylation in the ribosomal protein L16; in humans, Mina53 (MYC-induced nuclear antigen) and NO66 (Nucleolar protein 66) catalyze histidine-hydroxylation in ribosomal proteins rpL27a and rpL8, respectively. The functional assignments of the ROX open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in residue- and protein-selectivities of prokaryotic and eukaryotic ROX, crystal structures of ycfD and ycfDRM from E. coli and Rhodothermus marinus with those of human Mina53 and NO66 (hROX) reveal highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-oxygenases. ROX structures in complex with/without their substrates, support their functional assignments as hydroxylases, but not demethylases and reveal how the subfamily has evolved to catalyze the hydroxylation of different residue sidechains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-hydroxylases including the hypoxia-inducible factor asparaginyl-hydroxylase (FIH) and histone Nε-methyl lysine demethylases (KDMs) identifies branchpoints in 2OG-oxygenase evolution and distinguishes between JmjC-hydroxylases and -demethylases catalyzing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate oxidizing species reacts. This coordination flexibility has likely contributed to the evolution of the wide range of reactions catalyzed by iron-oxygenases.

MINA controls proliferation and tumorigenesis of glioblastoma by epigenetically regulating cyclins and CDKs via H3K9me3 demethylation

“…18 Structurally, MINA protein contains a conserved jumonji C (JmjC) domain that belongs to the histone demethylases family. 19 It has been reported that MINA is involved in reducing the trimethylation of histone H3K9 (H3K9me3). 10,20 Histone demethylases are known to regulate gene transcription by altering the methylate status on histones, 21 but their roles in cancers and the underlying molecular mechanisms are still unclear.…”

Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily

“…Our structural studies exploited catalytically inactive Ni 2+ -substituted enzymes to minimize oxidative damage to the enzyme. This strategy has been used with great success in investigations of Fe(II)/AKG-dependent oxygenases, for example, in the histone demethylases (23)(24)(25). Other work has demonstrated that metal substitution does not alter the coordination within the error of crystallographic resolution (26).…”

Structural definitions of Jumonji family demethylase selectivity

“…Nevertheless, Chowdhury et al recently reported on structural differences within the Jmj family, for example between the ROX enzyme NO66 and KDM4A [36]. More specifically, KDM family members only remove methyl groups from the terminal nitrogen of lysine side-chains, therefore their target residues do not penetrate as far into the active site.…”

“…ROXs and certain hydroxylases, such as FIH, form homodimers through interactions between alpha helical dimerisation domains and this oligomerisation is important for protein activity [36]. [39].…”