Family Search for PF01982 (CTP-dep_RFKase)

PF01982 hits 16 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

A0A0K1E2F9 CTP-dependent riboflavin kinase (EC 2.7.1.161) from Pyrobaculum sp. WP30 (see paper)
Aligns to 88:208 / 210 (57.6%), covers 100.0% of PF01982, 154.5 bits

Nmag_0941 CTP-dependent riboflavin kinase from Natrialba magadii ATCC 43099
Aligns to 105:231 / 235 (54.0%), covers 100.0% of PF01982, 151.4 bits

• A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T
  Siddaramappa, BMC genomics 2012
  • “...the riboflavin biosynthesis pathway were identified in Nab . magadii and only two of these (Nmag_0941 and 0942) were clustered together (Table 2). Vitamin B 3 (nicotinic acid) is the central component of coenzymes NAD and NADP, which are essential redox cofactors in metabolism. Like most...”

HISP_01730 DUF120 domain-containing protein from Haloarcula hispanica N601
Aligns to 105:230 / 232 (54.3%), covers 100.0% of PF01982, 151.3 bits

• Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica
  Lee, MicrobiologyOpen 2020
  • “...metabolism 3'phosphoadenosine 5'phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes 0.324 1.142 0.922 0.104 M HISP_01730 METABOLISM Metabolism of cofactors and vitamins CTPdependent riboflavin kinase 0.055 0.401 0.235 0.111 M HISP_04880 METABOLISM Energy production and conversion NADdependent aldehyde dehydrogenases 0.109 0.687 0.769 1.566 M HISP_09835 METABOLISM...”
  • “...include those involved in amino acid metabolism (e.g., HISP_04735, glutamate synthase; COG=E), coenzyme synthesis (e.g., HISP_01730, riboflavin kinase, COG=H), uptake transporters for phosphate/phosphonate (e.g., HISP_17215, COG=P), lipids (e.g., HISP_11670, COG=I), and sugars (HISP_18900, COG=G), as well as genes coding for proteins involved in energy production/conversion (e.g.,...”

rrnAC3074 unknown from Haloarcula marismortui ATCC 43049
Aligns to 193:318 / 320 (39.4%), covers 100.0% of PF01982, 150.2 bits

• Genome information management and integrated data analysis with HaloLex
  Pfeiffer, Archives of microbiology 2008
  • “...NP6028A rrnAC3062 954 1,032 Shortened rrnAC1698, OE1358R, HQ2259A rrnAC3071 915 1,149 Shortened OE3959R, HQ3234A, NP5036A rrnAC3074 699 963 Shortened NP0072A, HQ3236A, OE3964R rrnAC3079 573 624 Shortened NP3402A rrnAC3083 375 423 Shortened NP0948A, OE4292F, HQ3465A rrnAC3100 2,010 2,049 Shortened NP2262A, HQ1094A, OE3832F rrnAC3121 651 1,194 Shortened HQ1495A...”

WP_062266039 DUF120 domain-containing protein from Methanoculleus bourgensis
Aligns to 99:219 / 222 (54.5%), covers 100.0% of PF01982, 149.8 bits

• Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms
  Martinez-Liu, PloS one 2021
  • “...in archaeal TFs but not in bacteria ( Fig 5 ). For instance, the TFs WP_062266039 of Methanoculleus bourgensis , classified as a member of the MarR family, also contains a protein/riboflavin kinase activity (2.7.1.161), and WP_056934426 identified in Thermococcus barophilus , which performs a role...”

Q9HJA6 CTP-dependent riboflavin kinase (EC 2.7.1.161) from Thermoplasma acidophilum (see paper)
Ta1064 conserved hypothetical protein from Thermoplasma acidophilum DSM 1728
Aligns to 99:218 / 220 (54.5%), covers 100.0% of PF01982, 149.6 bits

• The biology of thermoacidophilic archaea from the order Sulfolobales
  Lewis, FEMS microbiology reviews 2021
  • “...N.A. MLPTv RbkR MarR MarR MarRb ST1710 BAB59904b Ta1064 EHP68448.1d Saci 1107 Repression FadR TetR S. tokodaii T. volcanium T. acidophilum M. yellowstonensis S....”
• Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis
  Maruyama, Frontiers in microbiology 2020
  • “...pdxS Ta0522 P57692 50S ribosomal protein L10 34.6 rpl10 Ta0359 Q9HJA6 Riboflavin kinase 25 ribK Ta1064 Q9HIR5 30S ribosomal protein S3 24.7 rps3 Ta1265 Q9HL71 50S ribosomal protein L1 23.9 rpl1 Ta0360 P25156 Proteasome subunit alpha 25.8 psmA Ta1288 Q9HM16 Translation initiation factor 6 23.5 eif6...”
• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.
  Pfeiffer, Genes 2021
  • “...also predicted for MJ0699 6c pathway gap EC 3.1.3.104 6c HVO_0326 rbkR yes 37% TA1064 Q9HJA6 [ 236 ] 28073944 bifunctional as gene regulator and enzyme 6c HVO_0326 (cont.) yes/no 32% MJ0056 Q60365 [ 248 ] 18073108 enzyme only; lacks an N-terminal HTH domain 6c HVO_1015...”
• Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis
  Maruyama, Frontiers in microbiology 2020
  • “...5-phosphate synthase subunit PdxS 36.5 pdxS Ta0522 P57692 50S ribosomal protein L10 34.6 rpl10 Ta0359 Q9HJA6 Riboflavin kinase 25 ribK Ta1064 Q9HIR5 30S ribosomal protein S3 24.7 rps3 Ta1265 Q9HL71 50S ribosomal protein L1 23.9 rpl1 Ta0360 P25156 Proteasome subunit alpha 25.8 psmA Ta1288 Q9HM16 Translation...”
• A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea
  Rodionova, Nucleic acids research 2017
  • “...digestion with Ulp1 protease at 4C overnight. The rbkR gene from T. acidophilum (Uniprot accession Q9HJA6) cloned into a pSGX3 vector was obtained from the New York SGX Research Center for Structural Genomics. The T. acidophilum RbkR protein ( ta RbkR) was expressed with a C-terminal...”

5trdA / Q9HJA6 Structure of rbkr (riboflavin kinase) from thermoplasma acidophilum determined in complex with ctp and its cognate DNA operator
Aligns to 95:214 / 219 (54.8%), covers 100.0% of PF01982, 149.5 bits

• Ligands: dna; cytidine-5'-triphosphate (5trdA)

HVO_0326 hypothetical protein from Haloferax volcanii DS2
Aligns to 106:231 / 237 (53.2%), covers 100.0% of PF01982, 148.5 bits

• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...Q58110 [ 236 ] 28073944 also predicted for MJ0699 6c pathway gap EC 3.1.3.104 6c HVO_0326 rbkR yes 37% TA1064 Q9HJA6 [ 236 ] 28073944 bifunctional as gene regulator and enzyme 6c HVO_0326 (cont.) yes/no 32% MJ0056 Q60365 [ 248 ] 18073108 enzyme only; lacks an...”

CSP5_1177 DUF120 domain-containing protein from Cuniculiplasma divulgatum
Aligns to 106:225 / 229 (52.4%), covers 99.2% of PF01982, 142.8 bits

• Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum
  Bargiela, Microorganisms 2020
  • “...CSP5_0498). In the category Coenzyme transport and metabolism, GTP:adenosylcobinamide-phosphate guanylyltransferase (CSP5_1294), archaeal CTP-dependent riboflavin kinase (CSP5_1177) (Flavin biosynthesis II in archaea) and FMN-dependent dehydrogenase/L-lactate dehydrogenase/type II isopentenyl diphosphate isomerase (CSP5_0048) were expressed. Furthermore, proteins of category K (Transcription) were expressed, in particular, ribbon-helix-helix CopG family protein...”

H2C8H2 CTP-dependent riboflavin kinase (EC 2.7.1.161) from Metallosphaera yellowstonensis (see paper)
Aligns to 93:215 / 217 (56.7%), covers 99.2% of PF01982, 136.3 bits

TEU_09890 DUF120 domain-containing protein from Thermococcus eurythermalis
Aligns to 92:209 / 211 (55.9%), covers 100.0% of PF01982, 134.2 bits

• Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent
  Zhao, Frontiers in microbiology 2020
  • “...nucleoside diphosphate (TEU_09080), uridylate (TEU_04165), ribose (TEU_01625 and TEU_02660), and cofactors, i.e., NAD (TEU_02205), riboflavin (TEU_09890), and pantoate (TEU_01430). Among the total 12 kinases, only carbamate kinase (TEU_01535) was up-expressed, which is involved in the arginine biosynthesis ( Supplementary Data S4 ). These results indicated a...”

PF0988 hypothetical protein from Pyrococcus furiosus DSM 3638
Aligns to 94:211 / 212 (55.7%), covers 99.2% of PF01982, 134.0 bits

• Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile using transcriptomics and proteomics
  Grünberger, mBio 2023
  • “...operon (PF0061PF0064, log 2 FC: 4.5), potentially under the control of the transcriptional regulator RbkR (PF0988) ( 84 ). Among the cold-responsive solute-binding proteins CipA (log 2 FC: 1.5) and CipB (log 2 FC: 0.2), only the former was induced significantly during CS ( 83 )....”
  • “...predicted regulons like cobalamin biosynthesis regulation by CblrR (unknown), riboflavin biosynthesis operon regulation by RbkR (PF0988), and thiamin transport regulation by ThiR (PF0601) (Fig. S9 at https://doi.org/10.6084/m9.figshare.24006960.v1 ) ( 40 , 86 90 ). Many genes controlled by validated or yet unknown transcription factors exhibit significant...”
• A novel endonuclease that may be responsible for damaged DNA base repair in Pyrococcus furiosus
  Shiraishi, Nucleic acids research 2015
  • “...of the proteins, and the conservation of amino acid sequences in Archaea, the hypothetical proteins PF0988 (AAL81112.1, Figure 3 , slice 8), PF1551 (AAL81675.1, slice 4 and 5) and PF1862 (AAL81986.1, slice 8) became the leading candidates. The gene encoding PF0988 is located downstream of the...”

TK1272 predicted transcription regulator, containing Crp and DUF120 domains from Thermococcus kodakaraensis KOD1
Aligns to 92:209 / 211 (55.9%), covers 100.0% of PF01982, 133.5 bits

• The TK0271 Protein Activates Transcription of Aromatic Amino Acid Biosynthesis Genes in the Hyperthermophilic Archaeon Thermococcus kodakarensis
  Yamamoto, mBio 2019
  • “...genes that were expressed in these lanes were TK0063, TK0142, TK0169, TK0271, TK0888, TK1210, TK1227, TK1272, TK1339, TK1489, TK1881, TK1955, TK2190, and TK2229. We carried out the same experiments with other DNA probes and found that the TK0271 protein was the only protein that displayed specificity...”

rfk / Q60365 CTP-dependent riboflavin kinase (EC 2.7.1.161) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see 2 papers)
RIFK_METJA / Q60365 Riboflavin kinase; RFK; CTP-dependent riboflavin kinase; CTP:riboflavin 5'-phosphotransferase; Flavokinase; EC 2.7.1.161 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see 2 papers)
Q60365 CTP-dependent riboflavin kinase (EC 2.7.1.161) from Methanocaldococcus jannaschii (see 3 papers)
WP_064496379 CTP-dependent riboflavin kinase from Methanocaldococcus jannaschii DSM 2661
Aligns to 7:126 / 132 (90.9%), covers 99.2% of PF01982, 129.5 bits

• function: Catalyzes the CTP-dependent phosphorylation of riboflavin (vitamin B2) to form flavin mononucleotide (FMN). Can also utilize UTP as the phosphate donor, although less efficiently, and it is unclear if ATP and GTP can also serve as substrates (PubMed:18245297) or not (PubMed:18073108).
  catalytic activity: riboflavin + CTP = CDP + FMN + H(+) (RHEA:25021)
  cofactor: Mg(2+) (Binds 1 magnesium ion per subunit.) This ion is coordinated by a threonine and an asparagine, and by the alpha- and beta-phosphates of CDP
  subunit: Monomer.
• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...236 ] 28073944 bifunctional as gene regulator and enzyme 6c HVO_0326 (cont.) yes/no 32% MJ0056 Q60365 [ 248 ] 18073108 enzyme only; lacks an N-terminal HTH domain 6c HVO_1015 ribL yes 50% MJ1179 Q58579 [ 249 ] 20822113 3.7. Biosynthesis of Membrane Lipids, Bacterioruberin and Menaquinone...”
• Identification and characterization of an archaeon-specific riboflavin kinase
  Mashhadi, Journal of bacteriology 2008
  • “...gene at locus MJ0056 (Swiss-Prot accession number Q60365) was amplified by PCR from genomic DNA with oligonucleotide primers pMJ0056Fwd (5-GGTCA...”
• Identification and characterization of an archaeon-specific riboflavin kinase.
  Mashhadi, Journal of bacteriology 2008
  • GeneRIF: Data show that the unexpected features of the purified recombinant enzyme were its use of CTP as the phosphoryl donor and the absence of a requirement for added metal ion to catalyze the formation of FMN.
• A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.
  Ammelburg, Structure (London, England : 1993) 2007 (PubMed)
  • GeneRIF: The structure, substrate-binding mode, and catalytic activity of this CTP specific riboflavin kinase are reported. It is suggested that CTP specificity is a general feature of archaeal riboflavin kinases.

MJ0056 conserved hypothetical protein from Methanocaldococcus jannaschii DSM 2661
Aligns to 11:130 / 136 (88.2%), covers 99.2% of PF01982, 129.4 bits

• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...[ 236 ] 28073944 bifunctional as gene regulator and enzyme 6c HVO_0326 (cont.) yes/no 32% MJ0056 Q60365 [ 248 ] 18073108 enzyme only; lacks an N-terminal HTH domain 6c HVO_1015 ribL yes 50% MJ1179 Q58579 [ 249 ] 20822113 3.7. Biosynthesis of Membrane Lipids, Bacterioruberin and...”
• Identification and characterization of an archaeon-specific riboflavin kinase
  Mashhadi, Journal of bacteriology 2008
  • “...jannaschii has been identified as the product of the MJ0056 gene. Recombinant expression of the MJ0056 gene in Escherichia coli led to a large increase in the...”
  • “...of this archaeal riboflavin kinase. To date, orthologs of MJ0056 have been found only in archaea. It was noticed that the crystal structure of the MJ0056 gene...”
• A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels
  Ammelburg, Structure (London, England : 1993) 2007 (PubMed)
  • “...activity for one of these proteins, Methanocaldococcus jannaschii Mj0056, which is an archaeal riboflavin kinase. Mj0056 is unusual in utilizing CTP rather than...”
  • “...AMMELBURG M Introduction Results Bioinformatics Mj0056 Is a CTP-Dependent Archaeal Riboflavin Kinase Solution Structure of Apo-Mj0056...”

2oynA / Q60365 Crystal structure of cdp-bound protein mj0056 from methanococcus jannaschii, pfam duf120
Aligns to 12:131 / 137 (87.6%), covers 99.2% of PF01982, 129.3 bits

• Ligand: cytidine-5'-diphosphate (2oynA)

Or search for genetic data about PF01982 in the Fitness Browser