title: Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
abstract: 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.
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Rasheduzzaman
authors.initials: R
authors.lastname: Chowdhury
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Rok
authors.initials: R
authors.lastname: Sekirnik
authors.affiliation: Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, U.K.
authors.forename: Nigel C
authors.initials: NC
authors.lastname: Brissett
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Tobias
authors.initials: T
authors.lastname: Krojer
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Chia-Hua
authors.initials: CH
authors.lastname: Ho
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Stanley S
authors.initials: SS
authors.lastname: Ng
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Clifton
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Wei
authors.initials: W
authors.lastname: Ge
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Nadia J
authors.initials: NJ
authors.lastname: Kershaw
authors.affiliation: Synchrotron SOLEIL, Saint Aubin, 91192 Gif-sur-Yvette Cedex, France.
authors.forename: Gavin C
authors.initials: GC
authors.lastname: Fox
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Joao R C
authors.initials: JRC
authors.lastname: Muniz
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Melanie
authors.initials: M
authors.lastname: Vollmar
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Claire
authors.initials: C
authors.lastname: Phillips
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Ewa S
authors.initials: ES
authors.lastname: Pilka
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Kavanagh
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.
authors.forename: Frank
authors.initials: F
authors.lastname: von Delft
authors.affiliation: Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, U.K.|NIHR Oxford Biomedical Research Unit, Botnar Research Centre, Oxford OX3 7LD, UK.
authors.forename: Udo
authors.initials: U
authors.lastname: Oppermann
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Michael A
authors.initials: MA
authors.lastname: McDonough
authors.affiliation: Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, U.K.
authors.forename: Aiden J
authors.initials: AJ
authors.lastname: Doherty
authors.affiliation: The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Schofield
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D017124:Conserved Sequence; D056890:Eukaryota / Q000145:classification / Q000201:enzymology*; D006801:Humans; D008958:Models, Molecular; D010105:Oxygenases / Q000737:chemistry* / Q000378:metabolism; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000145:classification / Q000201:enzymology*; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D012270:Ribosomes / Q000201:enzymology*; D016415:Sequence Alignment
chemical_list: D010105:Oxygenases