BRENDA - Enzyme Database
show all sequences of 5.4.99.24

Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly

Leppik, M.; Liiv, A.; Remme, J.; Nucleic Acids Res. 45, 6098-6108 (2017)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression of chimeric enzyme mutants RluCD in Escherichia coli strains M15 and CD204, expression of chimeric pseudouridine synthase RluCD, under control of arabinose inducible araBAD promoter, interferes with ribosome formation in wild-type M15 strain and strain CD204 lacking RluC and RluD, while cells transformed with catalytically inactive RluCD (RluCD D139N) and empty vector (pQE60), used as a controls, represent a normal ribosomal profile in sucrose density gradient. Strain CD204 contains a mutant form of RF-2 (D131Y) that suppresses ribosome assembly defect caused by the deletion of the RluD. Strain rluD114 where yfiI (RluD) gene has been disrupted with Km cassette is used as a parent strain to construct strain CD204
Escherichia coli
Engineering
Amino acid exchange
Commentary
Organism
D139N
site-directed mutagenesis of the chimeric enzyme mutant RluCD, the mutant is catalytically inactive
Escherichia coli
additional information
construction of a chimeric pseudouridine synthase (RluCD) containing the N-terminal S4 domain of enzyme RluC (EC 5.4.99.24) and the C-terminal catalytic domain of enzyme RluD (EC 5.4.99.23). The chimeric mutant is able to introduce excessive pseudouridines into rRNA at non-native positions. The chimeric enzyme RluCD is used as a tool to study an effect of over-modification of rRNA on the ribosome biogenesis. Excessive pseudouridylation of 23S rRNA reduces progression of ribosome assembly during early or middle stages. A modification interference approach identifies the sites in 23S rRNA whose modification prevents ribosome assembly. It is plausible that pseudouridines can cause RNA misfolding when present at non-native positions. RluCD isomerizes many uridines of rRNA in a non-specific manner. Induction of the RluCD at the exponential growth phase leads to severe inhibition of translation while transcription is only slightly affected
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
23S rRNA uridine955/uridine2504/uridine2580
Escherichia coli
-
23S rRNA pseudouridine955/pseudouridine2504/pseudouridine2580
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P0AA39
M15
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
23S rRNA uridine955/uridine2504/uridine2580
-
748788
Escherichia coli
23S rRNA pseudouridine955/pseudouridine2504/pseudouridine2580
-
-
-
?
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of chimeric enzyme mutants RluCD in Escherichia coli strains M15 and CD204, expression of chimeric pseudouridine synthase RluCD, under control of arabinose inducible araBAD promoter, interferes with ribosome formation in wild-type M15 strain and strain CD204 lacking RluC and RluD, while cells transformed with catalytically inactive RluCD (RluCD D139N) and empty vector (pQE60), used as a controls, represent a normal ribosomal profile in sucrose density gradient. Strain CD204 contains a mutant form of RF-2 (D131Y) that suppresses ribosome assembly defect caused by the deletion of the RluD. Strain rluD114 where yfiI (RluD) gene has been disrupted with Km cassette is used as a parent strain to construct strain CD204
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D139N
site-directed mutagenesis of the chimeric enzyme mutant RluCD, the mutant is catalytically inactive
Escherichia coli
additional information
construction of a chimeric pseudouridine synthase (RluCD) containing the N-terminal S4 domain of enzyme RluC (EC 5.4.99.24) and the C-terminal catalytic domain of enzyme RluD (EC 5.4.99.23). The chimeric mutant is able to introduce excessive pseudouridines into rRNA at non-native positions. The chimeric enzyme RluCD is used as a tool to study an effect of over-modification of rRNA on the ribosome biogenesis. Excessive pseudouridylation of 23S rRNA reduces progression of ribosome assembly during early or middle stages. A modification interference approach identifies the sites in 23S rRNA whose modification prevents ribosome assembly. It is plausible that pseudouridines can cause RNA misfolding when present at non-native positions. RluCD isomerizes many uridines of rRNA in a non-specific manner. Induction of the RluCD at the exponential growth phase leads to severe inhibition of translation while transcription is only slightly affected
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
23S rRNA uridine955/uridine2504/uridine2580
Escherichia coli
-
23S rRNA pseudouridine955/pseudouridine2504/pseudouridine2580
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
23S rRNA uridine955/uridine2504/uridine2580
-
748788
Escherichia coli
23S rRNA pseudouridine955/pseudouridine2504/pseudouridine2580
-
-
-
?
General Information
General Information
Commentary
Organism
malfunction
excessive pseudouridylation of 23S rRNA by the chimeric mutant RluCD reduces progression of ribosome assembly during early or middle stages. Modification of sites in 23S rRNA prevents ribosome assembly, interfering positions are located inside the ribosome, mapping. It is plausible that pseudouridines can cause RNA misfolding when present at non-native positions. Recombinant expression of RluCD protein itself inhibits ribosome assembly by binding to the precursor particles and blocking the assembly of r-proteins. The phenotypic effects are caused by the catalytic activity of the chimeric pseudouridine synthase RluCD, mechanism, overview. The excessive pseudouridines in rRNA species cause strong selection against 70S ribosome pool. Ribosome assembly defect causes degradation of unassembled rRNA and accumulation of small RNA fragments on the top of gradient
Escherichia coli
General Information (protein specific)
General Information
Commentary
Organism
malfunction
excessive pseudouridylation of 23S rRNA by the chimeric mutant RluCD reduces progression of ribosome assembly during early or middle stages. Modification of sites in 23S rRNA prevents ribosome assembly, interfering positions are located inside the ribosome, mapping. It is plausible that pseudouridines can cause RNA misfolding when present at non-native positions. Recombinant expression of RluCD protein itself inhibits ribosome assembly by binding to the precursor particles and blocking the assembly of r-proteins. The phenotypic effects are caused by the catalytic activity of the chimeric pseudouridine synthase RluCD, mechanism, overview. The excessive pseudouridines in rRNA species cause strong selection against 70S ribosome pool. Ribosome assembly defect causes degradation of unassembled rRNA and accumulation of small RNA fragments on the top of gradient
Escherichia coli
Other publictions for EC 5.4.99.24
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
748788
Leppik
Random pseuoduridylation in v ...
Escherichia coli
Nucleic Acids Res.
45
6098-6108
2017
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699543
Toh
An indigenous posttranscriptio ...
Escherichia coli
J. Mol. Biol.
380
593-597
2008
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704271
Jiang
Identification of novel Escher ...
Escherichia coli
J. Bacteriol.
189
3434-3444
2007
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1
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1
1
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702207
Mizutani
Crystal structures of the cata ...
Escherichia coli
Biochemistry
43
4454-4463
2004
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1
1
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1
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3
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5857
Corollo
-
Crystallisation and characteri ...
Escherichia coli
Acta Crystallogr. Sect. D
55
302-304
1999
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1
1
1
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1
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702195
Huang
Identification of two Escheric ...
Escherichia coli
Biochemistry
37
15951-15957
1998
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1
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704389
Conrad
The rluC gene of Escherichia c ...
Escherichia coli
J. Biol. Chem.
273
18562-18566
1998
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1
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