2-Oxoglutarate (2OG)-dependent
oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated
chromatin components and in the hydroxylation of
transcription factors and
splicing factor proteins. Recently, 2OG-dependent
oxygenases that catalyse hydroxylation of
transfer RNA and
ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. The finding that ribosomal
oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses
arginine hydroxylation in the
ribosomal protein L16; in humans, MYC-induced
nuclear antigen (MINA53; also known as MINA) and
nucleolar protein 66 (NO66) catalyse
histidine hydroxylation in the
ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and
protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent
oxygenases. ROX structures with and without their substrates support their functional assignments as
hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of
ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing
hydroxylases, including the
hypoxia-inducible factor asparaginyl
hydroxylase FIH and
histone N(ε)-
methyl lysine demethylases, identifies branch points in 2OG-dependent
oxygenase evolution and distinguishes between JmjC-containing
hydroxylases and demethylases catalysing 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 probably contributed to the evolution of the wide range of reactions catalysed by
oxygenases.