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Information on EC 2.7.1.161 - CTP-dependent riboflavin kinase
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2.7.1.161 CTP-dependent riboflavin kinaseIUBMB Comments
This archaeal enzyme differs from EC 2.7.1.26, riboflavin kinase, in using CTP as the donor nucleotide. UTP, but not ATP or GTP, can also act as a phosphate donor but it is at least an order of magnitude less efficient than CTP.
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The expected taxonomic range for this enzyme is: Archaea, Bacteria, Eukaryota
Synonyms
mj0056, ctp-dependent riboflavin kinase, methanocaldococcus jannaschii mj0056, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
myRbkR
RbkR
RibK
riboflavin kinase
taRbkR
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
CTP + riboflavin = CDP + FMN
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SYSTEMATIC NAME
IUBMB Comments
CTP:riboflavin 5′-phosphotransferase
This archaeal enzyme differs from EC 2.7.1.26, riboflavin kinase, in using CTP as the donor nucleotide. UTP, but not ATP or GTP, can also act as a phosphate donor but it is at least an order of magnitude less efficient than CTP.
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CAS REGISTRY NUMBER
COMMENTARY
9032-82-0
c.f. EC 2.7.1.26
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + riboflavin
ADP + FMN
30% of the activity with CTP
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-
?
ATP + riboflavin
ADP + riboflavin 5'-phosphate
30% of the activity with ATP
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-
?
GTP + riboflavin
GDP + FMN
11% of the activity with CTP
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-
?
GTP + riboflavin
GDP + riboflavin 5'-phosphate
11% of the activity with ATP
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-
?
UTP + riboflavin
UDP + FMN
activity with UTP is at least one order of magnitude less efficient
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-
?
CTP + riboflavin
CDP + FMN
at reaction temperatures of up to 85°C (the temperature of the natural habitat of Methanocaldococcus jannaschii) riboflavin is completely converted to FMN
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-
?
CTP + riboflavin
CDP + riboflavin 5'-phosphate
most active with CTP as the substrate
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-
?
CTP + riboflavin
CDP + riboflavin 5'-phosphate
utilizes CTP rather than ATP as the donor nucleotide
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?
additional information
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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additional information
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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additional information
?
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ATP and GTP do not support the production of FMN at 85°C
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?
additional information
?
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ATP and GTP do not support the production of FMN at 85°C
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?
additional information
?
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enzyme-DNA binding analysis using the recombinant enzyme, overview. FMN-free pyRbkR protein binds two DNA fragments containing candidate regulatory sites upstream of the arfA and ribB genes in Pyrobaculum yellowstonensis. Both DNA fragments demonstrate specific interaction with pyRbkR, with apparent EC50 values in the range of 20-40 nM
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additional information
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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additional information
?
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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additional information
?
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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additional information
?
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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additional information
?
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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additional information
?
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enzyme-DNA binding analysis using the recombinant enzyme, overview
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Zn2+
additional information
Mg2+
contains 4-5 mol of Mg2+ and 0.0013 mol of Zn2+ per mol of protein
Zn2+
contains 4-5 mol of Mg2+ and 0.0013 mol of Zn2+ per mol of protein
additional information
absence of a requirement for added metal ion to catalyze the formation of FMN
additional information
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absence of a requirement for added metal ion to catalyze the formation of FMN
additional information
purified recombinant enzyme shows no requirement for added metal ion to catalyze the formation of FMN
additional information
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purified recombinant enzyme shows no requirement for added metal ion to catalyze the formation of FMN
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
the FMN-bound enzyme does not show myRbkR concentration-dependent binding with any tested DNA fragment, suggesting that FMN has a disruptive effect on DNA binding
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additional information
FAD does not show any significant effect on enzyme-DNA interaction, while riboflavin and FMN substantially diminish the DNA binding affinity. Half-maximal EC50 of riboflavin and FMN are calculated to 144 nM and 41 nM, respectively, showing that FMN has a greater negative effect on the DNA-protein interactions
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
steady-state Michaelis-Menten kinetics
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additional information
additional information
steady-state Michaelis-Menten kinetics
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
evolution
prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
evolution
prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
evolution
prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
evolution
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prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
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evolution
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prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
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evolution
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prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
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evolution
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prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
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evolution
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prediction of RbkR operator sites and reconstruction of RbkR regulons in 94 archaeal genomes. While the identified RbkR operators show significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. Genetic and sequence comparisons. RbkR regulators in Archaea represent a distinct class of metabolite-sensing transcription factors emerging via fusion between DNA-binding and catalytic domains
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metabolism
analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
metabolism
analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
metabolism
analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
metabolism
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analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
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metabolism
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analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
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metabolism
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analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
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metabolism
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analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
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metabolism
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analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview
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physiological function
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain
physiological function
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain
physiological function
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. The riboflavin kinase domain of RbkRs serves not only as an essential function in the flavin biosynthesis but also as a sensor domain ofDNA-binding transcription factor
physiological function
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. The riboflavin kinase domain of RbkRs serves not only as an essential function in the flavin biosynthesis but also as a sensor domain ofDNA-binding transcription factor
physiological function
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riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain
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physiological function
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riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain
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physiological function
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riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain
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physiological function
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riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain
-
physiological function
-
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. The riboflavin kinase domain of RbkRs serves not only as an essential function in the flavin biosynthesis but also as a sensor domain ofDNA-binding transcription factor
-
physiological function
-
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. The riboflavin kinase domain of RbkRs serves not only as an essential function in the flavin biosynthesis but also as a sensor domain ofDNA-binding transcription factor
-
physiological function
-
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. The riboflavin kinase domain of RbkRs serves not only as an essential function in the flavin biosynthesis but also as a sensor domain ofDNA-binding transcription factor
-
physiological function
-
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. The riboflavin kinase domain of RbkRs serves not only as an essential function in the flavin biosynthesis but also as a sensor domain ofDNA-binding transcription factor
-
physiological function
-
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. The riboflavin kinase domain of RbkRs serves not only as an essential function in the flavin biosynthesis but also as a sensor domain ofDNA-binding transcription factor
-
physiological function
-
riboflavin kinase is an essential enzyme required for synthesis of FMN cofactor from vitamin B2. The bifunctional riboflavin kinase/regulator (RbkR) controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain
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additional information
the FMN binding site comprises residues Tyr115, Phe165, Pro185, Tyr190, and Glu195
additional information
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the FMN binding site comprises residues Tyr115, Phe165, Pro185, Tyr190, and Glu195
additional information
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the FMN binding site comprises residues Tyr115, Phe165, Pro185, Tyr190, and Glu195
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additional information
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the FMN binding site comprises residues Tyr115, Phe165, Pro185, Tyr190, and Glu195
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additional information
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the FMN binding site comprises residues Tyr115, Phe165, Pro185, Tyr190, and Glu195
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additional information
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the FMN binding site comprises residues Tyr115, Phe165, Pro185, Tyr190, and Glu195
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Show AA Sequence and Transmembrane Helices (2747 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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Mj0056 has sequence properties intermediate between basal cradle-loop barrels and ATP-dependent riboflavin kinases. It is proposed that it represents an evolutionary bridge between the two groups of proteins
additional information
Mj0056 has sequence properties intermediate between basal cradle-loop barrels and ATP-dependent riboflavin kinases. It is proposed that it represents an evolutionary bridge between the two groups of proteins
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
monomer
dimer
the conformations of the two monomers in the DNA-bound taRbkR dimer are similar with most of the differences arising from loop movements rather than domain movements
dimer
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the conformations of the two monomers in the DNA-bound taRbkR dimer are similar with most of the differences arising from loop movements rather than domain movements
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dimer
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the conformations of the two monomers in the DNA-bound taRbkR dimer are similar with most of the differences arising from loop movements rather than domain movements
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dimer
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the conformations of the two monomers in the DNA-bound taRbkR dimer are similar with most of the differences arising from loop movements rather than domain movements
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dimer
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the conformations of the two monomers in the DNA-bound taRbkR dimer are similar with most of the differences arising from loop movements rather than domain movements
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Mj0056 has sequence properties intermediate between basal cradle-loop barrels and ATP-dependent riboflavin kinases. It is proposed that it represents an evolutionary bridge between the two groups of proteins
Mj0056-MgCDP and Mj0056-MgCDP-FMN, in complex with natural reaction products and, Mj0056-NaCDP-PO4, with inorganic phosphate bound in a similar position as the FMN phosphate
structures, Mj0056-MgCDP and Mj0056-MgCDP-FMN, in complex with natural reaction products and a third, Mj0056-NaCDP-PO4, with inorganic phosphate
purified RbkR in complex with its specific DNA operator, X-ray diffraction structure determination and analysis. The asymmetric unit of the taRbkR-DNA-CTP complex structure contains a taRbkR dimer bound to an 18-bp RbkR site DNA
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
10 min at room temperature, followed by dilution in acetate buffer (pH 6.0)
the enzyme retains 40% (0.13 nmol/min) of its activity compared to the control (0.32 nmol/min) after treatment with 0.1 M HCl (pH 1.05) for
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain Rosetta2(DE3)pLysS by nickel affinity chromatography, gel filtration, hydrophobic interaction chhromatography, and ultrafiltration
recombinant N-terminally His6-Smt3-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, the His6-Smt3-tag is then cleaved from the purified RbkR protein by digestion with Ulp1 protease
recombinant N-terminally His6-Smt3-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, the His6-Smt3-tag is then cleaved from the purified RbkR protein by digestion with Ulp1 protease
recombinant N-terminally His6-Smt3-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, the His6-Smt3-tag is then cleaved from the purified RbkR protein by digestion with Ulp1 protease
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene ribK, genomic organization, recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain Rosetta2(DE3)pLysS
gene ribK, genomic organization, recombinant expression of N-terminally His6-Smt3-tagged enzyme in Escherichia coli strain BL21(DE3). The Smt3 polypeptide is a yeast SUMO orthologue which enhances protein solubility
recombinant expression of the MJ0056 gene in Escherichia coli
recombinant expression of the MJ0056 gene in Escherichia coli led to a large increase in the amount of flavin mononucleotide in the Escherichia coli cell extract
gene ribK, genomic organization, recombinant expression of N-terminally His6-Smt3-tagged enzyme in Escherichia coli strain BL21(DE3). The Smt3 polypeptide is a yeast SUMO orthologue which enhances protein solubility
gene ribK, genomic organization, recombinant expression of N-terminally His6-Smt3-tagged enzyme in Escherichia coli strain BL21(DE3). The Smt3 polypeptide is a yeast SUMO orthologue which enhances protein solubility