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Literature summary extracted from

  • Rodionova, I.A.; Vetting, M.W.; Li, X.; Almo, S.C.; Osterman, A.L.; Rodionov, D.A.
    A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea (2017), Nucleic Acids Res., 45, 3785-3799 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.7.1.161 gene ribK, genomic organization Methanocaldococcus jannaschii
2.7.1.161 gene ribK, genomic organization, recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain Rosetta2(DE3)pLysS Thermoplasma acidophilum
2.7.1.161 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 Pyrobaculum sp. WP30
2.7.1.161 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 Metallosphaera yellowstonensis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.1.161 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 Thermoplasma acidophilum

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.7.1.161 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 Metallosphaera yellowstonensis
2.7.1.161 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 Pyrobaculum sp. WP30

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.7.1.161 additional information
-
 additional information steady-state Michaelis-Menten kinetics Pyrobaculum sp. WP30
2.7.1.161 additional information
-
 additional information steady-state Michaelis-Menten kinetics Metallosphaera yellowstonensis
2.7.1.161 0.073
-
 riboflavin pH 8.0, 60°C, recombinant enzyme Pyrobaculum sp. WP30
2.7.1.161 0.09
-
 riboflavin pH 8.0, 60°C, recombinant enzyme Metallosphaera yellowstonensis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.1.161 Mg2+ required Methanocaldococcus jannaschii
2.7.1.161 Mg2+ required Thermoplasma acidophilum
2.7.1.161 Mg2+ required Pyrobaculum sp. WP30
2.7.1.161 Mg2+ required Metallosphaera yellowstonensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.1.161 CTP + riboflavin Methanocaldococcus jannaschii
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Thermoplasma acidophilum
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Pyrobaculum sp. WP30
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Metallosphaera yellowstonensis
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Methanocaldococcus jannaschii NBRC 100440
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Methanocaldococcus jannaschii DSM 2661
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Methanocaldococcus jannaschii ATCC 43067
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Methanocaldococcus jannaschii JAL-1
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Thermoplasma acidophilum JCM 9062
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Thermoplasma acidophilum AMRC-C165
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Metallosphaera yellowstonensis MK1
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Thermoplasma acidophilum ATCC 25905
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Thermoplasma acidophilum NBRC 15155
-
 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin Methanocaldococcus jannaschii JCM 10045
-
 CDP + FMN
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.1.161 Metallosphaera yellowstonensis H2C8H2
-
-
2.7.1.161 Metallosphaera yellowstonensis MK1 H2C8H2
-
-
2.7.1.161 Methanocaldococcus jannaschii Q60365 Methanococcus jannaschii
-
2.7.1.161 Methanocaldococcus jannaschii ATCC 43067 Q60365 Methanococcus jannaschii
-
2.7.1.161 Methanocaldococcus jannaschii DSM 2661 Q60365 Methanococcus jannaschii
-
2.7.1.161 Methanocaldococcus jannaschii JAL-1 Q60365 Methanococcus jannaschii
-
2.7.1.161 Methanocaldococcus jannaschii JCM 10045 Q60365 Methanococcus jannaschii
-
2.7.1.161 Methanocaldococcus jannaschii NBRC 100440 Q60365 Methanococcus jannaschii
-
2.7.1.161 Pyrobaculum sp. WP30 A0A0K1E2F9 Pyrobaculum yellowstonensis
-
2.7.1.161 Thermoplasma acidophilum Q9HJA6
-
-
2.7.1.161 Thermoplasma acidophilum AMRC-C165 Q9HJA6
-
-
2.7.1.161 Thermoplasma acidophilum ATCC 25905 Q9HJA6
-
-
2.7.1.161 Thermoplasma acidophilum JCM 9062 Q9HJA6
-
-
2.7.1.161 Thermoplasma acidophilum NBRC 15155 Q9HJA6
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.7.1.161 recombinant C-terminally His6-tagged enzyme from Escherichia coli strain Rosetta2(DE3)pLysS by nickel affinity chromatography, gel filtration, hydrophobic interaction chhromatography, and ultrafiltration Thermoplasma acidophilum
2.7.1.161 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 Pyrobaculum sp. WP30
2.7.1.161 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 Metallosphaera yellowstonensis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.1.161 CTP + riboflavin
-
 Methanocaldococcus jannaschii CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Thermoplasma acidophilum CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Pyrobaculum sp. WP30 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Metallosphaera yellowstonensis CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Methanocaldococcus jannaschii NBRC 100440 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Methanocaldococcus jannaschii DSM 2661 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Methanocaldococcus jannaschii ATCC 43067 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Methanocaldococcus jannaschii JAL-1 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Thermoplasma acidophilum JCM 9062 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Thermoplasma acidophilum AMRC-C165 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Metallosphaera yellowstonensis MK1 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Thermoplasma acidophilum ATCC 25905 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Thermoplasma acidophilum NBRC 15155 CDP + FMN
-
 ?
2.7.1.161 CTP + riboflavin
-
 Methanocaldococcus jannaschii JCM 10045 CDP + FMN
-
 ?
2.7.1.161 additional information enzyme-DNA binding analysis using the recombinant enzyme, overview Thermoplasma acidophilum ?
-
-
2.7.1.161 additional information enzyme-DNA binding analysis using the recombinant enzyme, overview Metallosphaera yellowstonensis ?
-
-
2.7.1.161 additional information 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 Pyrobaculum sp. WP30 ?
-
-
2.7.1.161 additional information enzyme-DNA binding analysis using the recombinant enzyme, overview Thermoplasma acidophilum JCM 9062 ?
-
-
2.7.1.161 additional information enzyme-DNA binding analysis using the recombinant enzyme, overview Thermoplasma acidophilum AMRC-C165 ?
-
-
2.7.1.161 additional information enzyme-DNA binding analysis using the recombinant enzyme, overview Metallosphaera yellowstonensis MK1 ?
-
-
2.7.1.161 additional information enzyme-DNA binding analysis using the recombinant enzyme, overview Thermoplasma acidophilum ATCC 25905 ?
-
-
2.7.1.161 additional information enzyme-DNA binding analysis using the recombinant enzyme, overview Thermoplasma acidophilum NBRC 15155 ?
-
-

Subunits

EC Number Subunits Comment Organism
2.7.1.161 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 Thermoplasma acidophilum

Synonyms

EC Number Synonyms Comment Organism
2.7.1.161 myRbkR
-
 Metallosphaera yellowstonensis
2.7.1.161 pyRbkR
-
 Pyrobaculum sp. WP30
2.7.1.161 RbkR
-
 Methanocaldococcus jannaschii
2.7.1.161 RbkR
-
 Thermoplasma acidophilum
2.7.1.161 RbkR
-
 Pyrobaculum sp. WP30
2.7.1.161 RbkR
-
 Metallosphaera yellowstonensis
2.7.1.161 RibK
-
 Methanocaldococcus jannaschii
2.7.1.161 RibK
-
 Thermoplasma acidophilum
2.7.1.161 RibK
-
 Pyrobaculum sp. WP30
2.7.1.161 RibK
-
 Metallosphaera yellowstonensis
2.7.1.161 riboflavin kinase UniProt Methanocaldococcus jannaschii
2.7.1.161 riboflavin kinase UniProt Thermoplasma acidophilum
2.7.1.161 riboflavin kinase UniProt Pyrobaculum sp. WP30
2.7.1.161 riboflavin kinase UniProt Metallosphaera yellowstonensis
2.7.1.161 taRbkR
-
 Methanocaldococcus jannaschii

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.7.1.161 60
-
-
 Pyrobaculum sp. WP30
2.7.1.161 60
-
-
 Metallosphaera yellowstonensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.7.1.161 8
-
 assay at Pyrobaculum sp. WP30
2.7.1.161 8
-
 assay at Metallosphaera yellowstonensis

Cofactor

EC Number Cofactor Comment Organism Structure
2.7.1.161 CTP
-
 Methanocaldococcus jannaschii
2.7.1.161 CTP
-
 Thermoplasma acidophilum
2.7.1.161 CTP
-
 Pyrobaculum sp. WP30
2.7.1.161 CTP
-
 Metallosphaera yellowstonensis

General Information

EC Number General Information Comment Organism
2.7.1.161 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 Thermoplasma acidophilum
2.7.1.161 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 Pyrobaculum sp. WP30
2.7.1.161 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 Metallosphaera yellowstonensis
2.7.1.161 evolution RbkRs genetic and sequence comparisons Methanocaldococcus jannaschii
2.7.1.161 metabolism analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview Thermoplasma acidophilum
2.7.1.161 metabolism analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview Pyrobaculum sp. WP30
2.7.1.161 metabolism analysis of the mechanism of the RbkR-mediated transcriptional regulation of riboflavin metabolism in Archaea, overview Metallosphaera yellowstonensis
2.7.1.161 additional information the FMN binding site comprises residues Tyr115, Phe165, Pro185, Tyr190, and Glu195 Thermoplasma acidophilum
2.7.1.161 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 Methanocaldococcus jannaschii
2.7.1.161 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 Pyrobaculum sp. WP30
2.7.1.161 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 Thermoplasma acidophilum
2.7.1.161 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 Metallosphaera yellowstonensis