ID H3DN54_TETNG Unreviewed; 312 AA.
AC H3DN54;
DT 18-APR-2012, integrated into UniProtKB/TrEMBL.
DT 18-APR-2012, sequence version 1.
DT 27-MAR-2024, entry version 53.
DE RecName: Full=Ribokinase {ECO:0000256|ARBA:ARBA00016943, ECO:0000256|HAMAP-Rule:MF_03215};
DE Short=RK {ECO:0000256|HAMAP-Rule:MF_03215};
DE EC=2.7.1.15 {ECO:0000256|ARBA:ARBA00012035, ECO:0000256|HAMAP-Rule:MF_03215};
GN Name=RBKS {ECO:0000256|HAMAP-Rule:MF_03215};
OS Tetraodon nigroviridis (Spotted green pufferfish) (Chelonodon
OS nigroviridis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata;
OC Eupercaria; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Tetraodon.
OX NCBI_TaxID=99883 {ECO:0000313|Ensembl:ENSTNIP00000021953.1, ECO:0000313|Proteomes:UP000007303};
RN [1] {ECO:0000313|Proteomes:UP000007303}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15496914; DOI=10.1038/nature03025;
RA Jaillon O., Aury J.-M., Brunet F., Petit J.-L., Stange-Thomann N.,
RA Mauceli E., Bouneau L., Fischer C., Ozouf-Costaz C., Bernot A., Nicaud S.,
RA Jaffe D., Fisher S., Lutfalla G., Dossat C., Segurens B., Dasilva C.,
RA Salanoubat M., Levy M., Boudet N., Castellano S., Anthouard V., Jubin C.,
RA Castelli V., Katinka M., Vacherie B., Biemont C., Skalli Z., Cattolico L.,
RA Poulain J., De Berardinis V., Cruaud C., Duprat S., Brottier P.,
RA Coutanceau J.-P., Gouzy J., Parra G., Lardier G., Chapple C.,
RA McKernan K.J., McEwan P., Bosak S., Kellis M., Volff J.-N., Guigo R.,
RA Zody M.C., Mesirov J., Lindblad-Toh K., Birren B., Nusbaum C., Kahn D.,
RA Robinson-Rechavi M., Laudet V., Schachter V., Quetier F., Saurin W.,
RA Scarpelli C., Wincker P., Lander E.S., Weissenbach J., Roest Crollius H.;
RT "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the
RT early vertebrate proto-karyotype.";
RL Nature 431:946-957(2004).
RN [2] {ECO:0000313|Ensembl:ENSTNIP00000021953.1}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (NOV-2023) to UniProtKB.
CC -!- FUNCTION: Catalyzes the phosphorylation of ribose at O-5 in a reaction
CC requiring ATP and magnesium. The resulting D-ribose-5-phosphate can
CC then be used either for sythesis of nucleotides, histidine, and
CC tryptophan, or as a component of the pentose phosphate pathway.
CC {ECO:0000256|HAMAP-Rule:MF_03215}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + D-ribose = ADP + D-ribose 5-phosphate + H(+);
CC Xref=Rhea:RHEA:13697, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:47013, ChEBI:CHEBI:78346, ChEBI:CHEBI:456216;
CC EC=2.7.1.15; Evidence={ECO:0000256|ARBA:ARBA00000691,
CC ECO:0000256|HAMAP-Rule:MF_03215};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_03215};
CC Note=Requires a divalent cation, most likely magnesium in vivo, as an
CC electrophilic catalyst to aid phosphoryl group transfer. It is the
CC chelate of the metal and the nucleotide that is the actual substrate.
CC {ECO:0000256|HAMAP-Rule:MF_03215};
CC -!- ACTIVITY REGULATION: Activated by a monovalent cation that binds near,
CC but not in, the active site. The most likely occupant of the site in
CC vivo is potassium. Ion binding induces a conformational change that may
CC alter substrate affinity. {ECO:0000256|HAMAP-Rule:MF_03215}.
CC -!- PATHWAY: Carbohydrate metabolism; D-ribose degradation; D-ribose 5-
CC phosphate from beta-D-ribopyranose: step 2/2. {ECO:0000256|HAMAP-
CC Rule:MF_03215}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_03215}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_03215}.
CC Nucleus {ECO:0000256|HAMAP-Rule:MF_03215}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family. Ribokinase
CC subfamily. {ECO:0000256|HAMAP-Rule:MF_03215}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_03215}.
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DR AlphaFoldDB; H3DN54; -.
DR STRING; 99883.ENSTNIP00000021953; -.
DR Ensembl; ENSTNIT00000022189.1; ENSTNIP00000021953.1; ENSTNIG00000018772.1.
DR GeneTree; ENSGT00390000005743; -.
DR HOGENOM; CLU_027634_2_3_1; -.
DR InParanoid; H3DN54; -.
DR OMA; DIVLIQQ; -.
DR TreeFam; TF105770; -.
DR UniPathway; UPA00916; UER00889.
DR Proteomes; UP000007303; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004747; F:ribokinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019303; P:D-ribose catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006753; P:nucleoside phosphate metabolic process; IEA:UniProt.
DR CDD; cd01174; ribokinase; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR HAMAP; MF_01987; Ribokinase; 1.
DR InterPro; IPR002173; Carboh/pur_kinase_PfkB_CS.
DR InterPro; IPR011877; D_ribokin.
DR InterPro; IPR011611; PfkB_dom.
DR InterPro; IPR002139; Ribo/fructo_kinase.
DR InterPro; IPR029056; Ribokinase-like.
DR NCBIfam; TIGR02152; D_ribokin_bact; 1.
DR PANTHER; PTHR10584:SF166; RIBOKINASE; 1.
DR PANTHER; PTHR10584; SUGAR KINASE; 1.
DR Pfam; PF00294; PfkB; 1.
DR PRINTS; PR00990; RIBOKINASE.
DR SUPFAM; SSF53613; Ribokinase-like; 1.
DR PROSITE; PS00584; PFKB_KINASES_2; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_03215};
KW Carbohydrate metabolism {ECO:0000256|HAMAP-Rule:MF_03215};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_03215};
KW Kinase {ECO:0000256|HAMAP-Rule:MF_03215, ECO:0000256|RuleBase:RU003704};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_03215};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_03215}; Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_03215};
KW Nucleus {ECO:0000256|HAMAP-Rule:MF_03215};
KW Potassium {ECO:0000256|ARBA:ARBA00022958, ECO:0000256|HAMAP-Rule:MF_03215};
KW Reference proteome {ECO:0000313|Proteomes:UP000007303};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_03215}.
FT DOMAIN 7..302
FT /note="Carbohydrate kinase PfkB"
FT /evidence="ECO:0000259|Pfam:PF00294"
FT ACT_SITE 259
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 15..17
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 143
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 188
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 224..229
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 253
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 255
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 258..259
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 259
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 285
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 291
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 294
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 296
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 300
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
SQ SEQUENCE 312 AA; 32899 MW; 450504885E4A25BA CRC64;
MAEETFDVMV VGSCMTDMVS QAPRLPKAGE TIHGLKFFTG FGGKGNQCVQ AARLGAKTTM
VCKVGKDIFG DNYIQNFKDN GVHTDFVGQT SDAATGAASI IVNNAGENAI VIVAGANMLL
NRADLQEALP AITRSKVMVC QLEIHPQISL QALRMAQKNN GYNMRFARLA CARLDADFYT
TSDVFCCNES EAEMLTGSAV TSVEEAGEAA AELLRRGCKS VVVTLGPQGC VVLQARGSAP
KHVPTAAPVT AVDTTGAGDC FIGALAFYMA HYPTMALEEM AHRANQVAGV SVQAAGTQTS
FPFRADLPAA LF
//
