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Information on EC 1.14.11.47 - [50S ribosomal protein L16]-arginine 3-hydroxylase
for references in articles please use BRENDA:EC1.14.11.47
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EC Tree 1 Oxidoreductases
1.14 Acting on paired donors, with incorporation or reduction of molecular oxygen
1.14.11 With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
1.14.11.47 [50S ribosomal protein L16]-arginine 3-hydroxylase
IUBMB Comments
The enzyme, characterized from the bacterium Escherichia coli, hydroxylates an arginine residue on the 50S ribosomal protein L16, and is involved in regulation of bacterial ribosome assembly.
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
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[50S ribosomal protein L16]-L-Arg81
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[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81
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Synonyms
50S ribosomal protein L16 arginine hydroxylase, ycfD, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ycfD
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2 = [50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
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SYSTEMATIC NAME
IUBMB Comments
[50S ribosomal protein L16]-L-Arg81,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
The enzyme, characterized from the bacterium Escherichia coli, hydroxylates an arginine residue on the 50S ribosomal protein L16, and is involved in regulation of bacterial ribosome assembly.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
AVSEATIR + 2-oxoglutarate + O2
[AVSEATIR]-(3R)-3-hydroxy-L-Arg8 + succinate + CO2
Substrates: -
Products: -
Products: -
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KPITEKPLAVRMGKGKGNVE + 2-oxoglutarate + O2
[KPITEKPLAVRMGKGKGNVE]-(3R)-3-hydroxy-L-Arg11 + succinate + CO2
Substrates: peptide derived from 50S ribosomal protein L16
Products: -
Products: -
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RLLPAVSEATIRRL + 2-oxoglutarate + O2
[RLLPAVSEATIRRL]-(3R)-3-hydroxy-L-Arg12 + succinate + CO2
Substrates: -
Products: modification occurs at the arginine at the -3 position relative to the C-terminus
Products: modification occurs at the arginine at the -3 position relative to the C-terminus
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[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-L-Arg82 + 2-oxoglutarate + O2
[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-(3R)-3-hydroxy-L-Arg82 + succinate + CO2
[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-L-Arg + 2-oxoglutarate + O2
[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-(3R)-3-hydroxy-L-Arg + succinate + CO2
[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
[50S ribosomal protein L16]-L-Arg82 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg82 + succinate + CO2
[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-L-Arg82 + 2-oxoglutarate + O2
[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-(3R)-3-hydroxy-L-Arg82 + succinate + CO2
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Substrates: -
Products: -
Products: -
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[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-L-Arg82 + 2-oxoglutarate + O2
[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-(3R)-3-hydroxy-L-Arg82 + succinate + CO2
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Substrates: -
Products: -
Products: -
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[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-L-Arg + 2-oxoglutarate + O2
[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-(3R)-3-hydroxy-L-Arg + succinate + CO2
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Substrates: -
Products: -
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[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-L-Arg + 2-oxoglutarate + O2
[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-(3R)-3-hydroxy-L-Arg + succinate + CO2
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Substrates: -
Products: -
Products: -
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[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
Substrates: -
Products: -
Products: -
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[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
Substrates: -
Products: more than 95% hydoxylation, residue Arg81 is the only residue observed to be hydroxylated
Products: more than 95% hydoxylation, residue Arg81 is the only residue observed to be hydroxylated
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[50S ribosomal protein L16]-L-Arg82 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg82 + succinate + CO2
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Substrates: -
Products: -
Products: -
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[50S ribosomal protein L16]-L-Arg82 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg82 + succinate + CO2
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Substrates: -
Products: -
Products: -
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additional information
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Substrates: binding of 2-oxoglutarate to isoform YcfD occurs in an exothermic manner, dissociation constant is 55.6 microM. Residues S116 and R140 are involved in binding
Products: -
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additional information
?
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Substrates: of the tested peptides, six or more residues are required for efficient hydroxylation. Hydroxylation is ablated when the C-terminus is extended to more closely resemble a protein. Hydroxylation occurs with incorporation of more than 90% 18O from 18O2 and occurs at C-3 of arginine leaing to a stereochemistry of the hydroxylated arginine of 2S,3R
Products: -
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additional information
?
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Substrates: enzyme displays a temperature-dependent variation in uL16 hydroxylation. Dioxygen availability can be a limiting factor for ycfD catalysis at high temperatures, consistent with incomplete uL16 hydroxylation observed
Products: -
Products: -
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additional information
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Substrates: enzyme displays a temperature-dependent variation in uL16 hydroxylation. Dioxygen availability can be a limiting factor for ycfD catalysis at high temperatures, consistent with incomplete uL16 hydroxylation observed
Products: -
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
Substrates: -
Products: -
Products: -
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Iron
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Fe(II)-coordinating triad consists of H133, D135, H196. Km value at 37°C is 0.0146 mM
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.075
[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-L-Arg82
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pH 7.5, 37°C
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0.208
[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-L-Arg
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pH 7.5, 37°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.47
[50S ribosomal cyclic peptide 6KKPAEVRMGKGKG88-linker]-L-Arg82
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pH 7.5, 37°C
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0.5
[50S ribosomal peptide KPVTKKPAEVRMGKGKGSVE-NH2]-L-Arg
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pH 7.5, 37°C
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
overexpression of L16 arginine hydroxylase YcfD inhibits cell growth signifying a toxic effect on ribosome assembly. The enzyme interacts with ribosomal protein RL-16 of the 50S subunit
physiological function
the enzyme plays a role in cell growth regulation
Show AA Sequence and Transmembrane Helices (304 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant E146A/K147A, predicted to enhance crystallizability, to 2.7 A resolution, space group P43212 with a single protein molecule in the asymmetric unit. The N-terminal domain contains the signature DSBH or beta-barrel that is characteristic of 2OG-dependent oxygenases. The core DSBH is made up of two beta-sheets, one composed of five strands and the second one composed of three strands
to 2.6 A resolution. Comparison with crystal structures of human MYC-induced nuclear antigen MINA53 and nucleolar protein NO66 as well as Rhodothermus marinus YcfD. The observed modes of ribosomal oxygenases hydroxylations have probably evolved into those of other JmjC-containing hydroxylases and the histoneNepsilon-methyl lysine demethylases, both by altering the coordination position from which the ferryl-oxo reacts and by engineering the depth of substrate penetration
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Van Staalduinen, L.; Novakowski, S.; Jia, Z.
Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe2+-dependent oxygenase involved in translational regulation in Escherichia coli
J. Mol. Biol.
426
1898-1910
2014
Escherichia coli (P27431)
brenda
Ge, W.; Wolf, A.; Feng, T.; Ho, C.; Sekirnik, R.; Zayer, A.; Granatino, N.; Cockman, M.; Loenarz, C.; Loik, N.; Hardy, A.; Claridge, T.; Hamed, R.; Chowdhury, R.; Gong, L.; Robinson, C.; Trudgian, D.; Jiang, M.; MacKeen, M.; McCullagh, J.; Gordiyenko, Y.;
Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans
Nat. Chem. Biol.
8
960-962
2012
Escherichia coli (P27431)
brenda
Chowdhury, R.; Sekirnik, R.; Brissett, N.; Krojer, T.; Ho, C.; Ng, S.; Clifton, I.; Ge, W.; Kershaw, N.; Fox, G.; Muniz, J.; Vollmar, M.; Phillips, C.; Pilka, E.; Kavanagh, K.; von Delft, F.; Oppermann, U.; McDonough, M.; Doherty, A.; Schofield, C.
Ribosomal oxygenases are structurally conserved from prokaryotes to humans
Nature
510
422-426
2014
Escherichia coli (P27431)
brenda
van Staalduinen, L.M.; Jia, Z.
Post-translational hydroxylation by 2OG/Fe(II)-dependent oxygenases as a novel regulatory mechanism in bacteria
Front. Microbiol.
5
798
2014
Escherichia coli (P27431)
brenda
Sekirnik, R.; Wilkins, S.; Bush, J.; Tarhonskaya, H.; Münzel, M.; Hussein, A.; Flashman, E.; Mohammed, S.; McDonough, M.; Loenarz, C.; Schofield, C.
YcfDRM is a thermophilic oxygen-dependent ribosomal protein uL16 oxygenase
Extremophiles
22
553-562
2018
Rhodothermus marinus, Rhodothermus marinus DSM 4252
brenda
EXTERNAL LINKS (specific for EC-Number 1.14.11.47)
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Release 2023.1 (January 2023)
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