Information on EC 1.14.11.47 - 50S ribosomal protein L16 3-hydroxylase

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The expected taxonomic range for this enzyme is: Escherichia coli

EC NUMBER
COMMENTARY hide
1.14.11.47
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RECOMMENDED NAME
GeneOntology No.
50S ribosomal protein L16 3-hydroxylase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2 = [50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
show the reaction diagram
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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.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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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
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
AVSEATIR + 2-oxoglutarate + O2
[AVSEATIR]-(3R)-3-hydroxy-L-Arg8 + succinate + CO2
show the reaction diagram
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?
KPITEKPLAVRMGKGKGNVE + 2-oxoglutarate + O2
[KPITEKPLAVRMGKGKGNVE]-(3R)-3-hydroxy-L-Arg11 + succinate + CO2
show the reaction diagram
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peptide derived from 50S ribosomal protein L16
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?
RLLPAVSEATIRRL + 2-oxoglutarate + O2
[RLLPAVSEATIRRL]-(3R)-3-hydroxy-L-Arg12 + succinate + CO2
show the reaction diagram
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modification occurs at the arginine at the -3 position relative to the C-terminus
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?
[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
show the reaction diagram
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more than 95% hydoxylation, residue Arg81 is the only residue observed to be hydroxylated
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?
additional information
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
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
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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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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E146A/K147A
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mutation predicted to enhance crystallizability
R140A
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loss of binding of 2-oxoglutarate
S116A
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loss of binding of 2-oxoglutarate