RIFK_METJA
ID RIFK_METJA Reviewed; 132 AA.
AC Q60365;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 05-APR-2011, sequence version 2.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Riboflavin kinase;
DE Short=RFK;
DE EC=2.7.1.161;
DE AltName: Full=CTP-dependent riboflavin kinase;
DE AltName: Full=CTP:riboflavin 5'-phosphotransferase;
DE AltName: Full=Flavokinase;
GN Name=ribK; OrderedLocusNames=MJ0056;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY,
RP GENE NAME, MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=18245297; DOI=10.1128/jb.01900-07;
RA Mashhadi Z., Zhang H., Xu H., White R.H.;
RT "Identification and characterization of an archaeon-specific riboflavin
RT kinase.";
RL J. Bacteriol. 190:2615-2618(2008).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH CDP.
RG New York structural genomics research consortium (NYSGRC);
RT "Crystal structure of hypothetical protein from Methanococcus jannaschii
RT bound to CDP.";
RL Submitted (MAR-2007) to the PDB data bank.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP REACTION PRODUCTS AND MAGNESIUM, STRUCTURE BY NMR, FUNCTION, CATALYTIC
RP ACTIVITY, CHARACTERIZATION, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RX PubMed=18073108; DOI=10.1016/j.str.2007.09.027;
RA Ammelburg M., Hartmann M.D., Djuranovic S., Alva V., Koretke K.K.,
RA Martin J., Sauer G., Truffault V., Zeth K., Lupas A.N., Coles M.;
RT "A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution
RT of cradle-loop barrels.";
RL Structure 15:1577-1590(2007).
CC -!- FUNCTION: Catalyzes the CTP-dependent phosphorylation of riboflavin
CC (vitamin B2) to form flavin mononucleotide (FMN). Can also utilize UTP
CC as the phosphate donor, although less efficiently, and it is unclear if
CC ATP and GTP can also serve as substrates (PubMed:18245297) or not
CC (PubMed:18073108). {ECO:0000269|PubMed:18073108,
CC ECO:0000269|PubMed:18245297}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=CTP + riboflavin = CDP + FMN + H(+); Xref=Rhea:RHEA:25021,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:37563, ChEBI:CHEBI:57986,
CC ChEBI:CHEBI:58069, ChEBI:CHEBI:58210; EC=2.7.1.161;
CC Evidence={ECO:0000269|PubMed:18073108, ECO:0000269|PubMed:18245297};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 magnesium ion per subunit. This ion is coordinated by a
CC threonine and an asparagine, and by the alpha- and beta-phosphates of
CC CDP.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=159 uM for riboflavin {ECO:0000269|PubMed:18245297};
CC KM=1.8 mM for CTP {ECO:0000269|PubMed:18245297};
CC Vmax=1.3 umol/min/mg enzyme {ECO:0000269|PubMed:18245297};
CC -!- PATHWAY: Cofactor biosynthesis; FMN biosynthesis; FMN from riboflavin
CC (CTP route): step 1/1.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:18073108,
CC ECO:0000269|PubMed:18245297, ECO:0000269|Ref.3}.
CC -!- MASS SPECTROMETRY: Mass=15218.1; Mass_error=10; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:18245297};
CC -!- SIMILARITY: Belongs to the archaeal riboflavin kinase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB98036.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; L77117; AAB98036.1; ALT_INIT; Genomic_DNA.
DR PIR; H64306; H64306.
DR RefSeq; WP_064496379.1; NC_000909.1.
DR PDB; 2OYN; X-ray; 1.85 A; A=1-132.
DR PDB; 2P3M; NMR; -; A=1-132.
DR PDB; 2VBS; X-ray; 3.00 A; A=1-132.
DR PDB; 2VBT; X-ray; 2.70 A; A=1-132.
DR PDB; 2VBU; X-ray; 1.70 A; A=1-132.
DR PDB; 2VBV; X-ray; 2.40 A; A/B=1-132.
DR PDBsum; 2OYN; -.
DR PDBsum; 2P3M; -.
DR PDBsum; 2VBS; -.
DR PDBsum; 2VBT; -.
DR PDBsum; 2VBU; -.
DR PDBsum; 2VBV; -.
DR AlphaFoldDB; Q60365; -.
DR BMRB; Q60365; -.
DR SMR; Q60365; -.
DR STRING; 243232.MJ_0056; -.
DR EnsemblBacteria; AAB98036; AAB98036; MJ_0056.
DR GeneID; 1450895; -.
DR KEGG; mja:MJ_0056; -.
DR eggNOG; arCOG01904; Archaea.
DR HOGENOM; CLU_140165_0_0_2; -.
DR InParanoid; Q60365; -.
DR OrthoDB; 91297at2157; -.
DR PhylomeDB; Q60365; -.
DR BioCyc; MetaCyc:MON-13864; -.
DR BRENDA; 2.7.1.161; 3260.
DR SABIO-RK; Q60365; -.
DR UniPathway; UPA00276; UER00929.
DR EvolutionaryTrace; Q60365; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008531; F:riboflavin kinase activity; IEA:InterPro.
DR GO; GO:0009398; P:FMN biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:InterPro.
DR Gene3D; 2.40.30.30; -; 1.
DR HAMAP; MF_01285; Riboflavin_kinase; 1.
DR InterPro; IPR039063; RibK_CTP-dep.
DR InterPro; IPR023470; Riboflavin_kinase_archaeal.
DR InterPro; IPR023602; Riboflavin_kinase_CTP-dep.
DR InterPro; IPR023465; Riboflavin_kinase_dom_sf.
DR PANTHER; PTHR40706; PTHR40706; 1.
DR Pfam; PF01982; CTP-dep_RFKase; 1.
DR SUPFAM; SSF82114; SSF82114; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Flavoprotein; FMN; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..132
FT /note="Riboflavin kinase"
FT /id="PRO_0000106673"
FT BINDING 10..15
FT /ligand="CDP"
FT /ligand_id="ChEBI:CHEBI:58069"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 39
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:18073108"
FT BINDING 41
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:18073108"
FT BINDING 95
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 96
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 103
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 108..111
FT /ligand="CDP"
FT /ligand_id="ChEBI:CHEBI:58069"
FT /evidence="ECO:0000269|Ref.3"
FT STRAND 1..8
FT /evidence="ECO:0007829|PDB:2VBU"
FT HELIX 13..18
FT /evidence="ECO:0007829|PDB:2VBU"
FT HELIX 21..31
FT /evidence="ECO:0007829|PDB:2VBU"
FT STRAND 40..48
FT /evidence="ECO:0007829|PDB:2VBU"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:2VBU"
FT STRAND 56..58
FT /evidence="ECO:0007829|PDB:2P3M"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:2VBU"
FT STRAND 66..68
FT /evidence="ECO:0007829|PDB:2VBU"
FT STRAND 71..80
FT /evidence="ECO:0007829|PDB:2VBU"
FT STRAND 83..93
FT /evidence="ECO:0007829|PDB:2VBU"
FT STRAND 99..105
FT /evidence="ECO:0007829|PDB:2VBU"
FT HELIX 110..113
FT /evidence="ECO:0007829|PDB:2VBU"
FT STRAND 121..127
FT /evidence="ECO:0007829|PDB:2VBU"
SQ SEQUENCE 132 AA; 15214 MW; 12B9AF1567F7D8B8 CRC64;
MIIEGEVVSG LGEGRYFLSL PPYKEIFKKI LGFEPYEGTL NLKLDREFDI NKFKYIETED
FEFNGKRFFG VKVLPIKILI GNKKIDGAIV VPKKTYHSSE IIEIIAPMKL REQFNLKDGD
VIKILIKGDK DE
