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Ribosomal oxygenases are structurally conserved from prokaryotes to humans
Rasheduzzaman Chowdhury1, Rok Sekirnik1, Nigel C Brissett2
1The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
Nature
|May 13, 2014
Summary
2-Oxoglutarate (2OG)-dependent oxygenases, known as ribosomal oxygenases (ROXs), hydroxylate ribosomal proteins, impacting translation. Structural analysis reveals conserved folds and novel dimerization, defining a new subfamily of oxygenases and highlighting evolutionary flexibility.
Area of Science:
- Biochemistry
- Structural Biology
- Evolutionary Biology
Background:
- 2-Oxoglutarate (2OG)-dependent oxygenases regulate gene expression and protein function through modifications like demethylation and hydroxylation.
- Recently identified ribosomal oxygenases (ROXs) are crucial for translation, cellular growth, and differentiation, occurring across diverse organisms.
- ROXs hydroxylate specific ribosomal proteins, including arginine in E. coli and histidine in humans, raising questions about their evolutionary and structural relationships.
Purpose of the Study:
- To investigate the structural and evolutionary relationships of ribosomal oxygenases (ROXs) across prokaryotes and eukaryotes.
- To elucidate the catalytic mechanisms and substrate specificities of ROXs.
- To understand the evolution of 2OG-dependent oxygenases and their diverse functions.
Main Methods:
- Comparative structural analysis of crystal structures of ROXs from E. coli, R. marinus, and humans (MINA53, NO66).
- Biochemical assays to confirm hydroxylase activity and substrate binding.
- Bioinformatic comparisons with other JmjC-domain-containing hydroxylases.
Main Results:
- ROXs share highly conserved folds and exhibit novel dimerization modes, defining a new subfamily of 2OG-dependent oxygenases.
- Structural data confirm ROXs function as hydroxylases, not demethylases, and reveal adaptations for hydroxylating different ribosomal protein residues.
- Evolutionary comparisons distinguish ROXs from other JmjC-domain hydroxylases, highlighting flexibility in iron-bound substrate-oxidizing species coordination as a driver of functional diversification.
Conclusions:
- Ribosomal oxygenases (ROXs) represent a distinct subfamily of 2OG-dependent oxygenases with conserved structures but varied substrate specificities.
- The evolution of ROXs demonstrates how changes in coordination chemistry can lead to new hydroxylation activities, expanding the repertoire of oxygenase functions.
- Understanding ROX structure and function offers potential therapeutic strategies targeting modified ribosomes.
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