ID A0A2V0NJT6_9CHLO Unreviewed; 794 AA.
AC A0A2V0NJT6;
DT 12-SEP-2018, integrated into UniProtKB/TrEMBL.
DT 12-SEP-2018, sequence version 1.
DT 27-MAR-2024, entry version 25.
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 ORFNames=Rsub_00229 {ECO:0000313|EMBL:GBF87518.1};
OS Raphidocelis subcapitata.
OC Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Chlorophyceae;
OC CS clade; Sphaeropleales; Selenastraceae; Raphidocelis.
OX NCBI_TaxID=307507 {ECO:0000313|EMBL:GBF87518.1, ECO:0000313|Proteomes:UP000247498};
RN [1] {ECO:0000313|EMBL:GBF87518.1, ECO:0000313|Proteomes:UP000247498}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NIES-35 {ECO:0000313|EMBL:GBF87518.1,
RC ECO:0000313|Proteomes:UP000247498};
RX PubMed=29795299; DOI=10.1038/s41598-018-26331-6;
RA Suzuki S., Yamaguchi H., Nakajima N., Kawachi M.;
RT "Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an
RT insight into genome evolution and environmental adaptations in the
RT Sphaeropleales.";
RL Sci. Rep. 8:8058-8058(2018).
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 -!- SIMILARITY: Belongs to the xylose isomerase family.
CC {ECO:0000256|ARBA:ARBA00005765}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_03215}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:GBF87518.1}.
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DR EMBL; BDRX01000001; GBF87518.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A2V0NJT6; -.
DR STRING; 307507.A0A2V0NJT6; -.
DR InParanoid; A0A2V0NJT6; -.
DR UniPathway; UPA00916; UER00889.
DR Proteomes; UP000247498; 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:0009045; F:xylose isomerase activity; IEA:InterPro.
DR GO; GO:0019303; P:D-ribose catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.1190.20; -; 1.
DR Gene3D; 3.20.20.150; Divalent-metal-dependent TIM barrel enzymes; 1.
DR HAMAP; MF_01987; Ribokinase; 1.
DR InterPro; IPR011877; D_ribokin.
DR InterPro; IPR011611; PfkB_dom.
DR InterPro; IPR002139; Ribo/fructo_kinase.
DR InterPro; IPR029056; Ribokinase-like.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR InterPro; IPR001998; Xylose_isomerase.
DR PANTHER; PTHR10584:SF166; RIBOKINASE; 1.
DR PANTHER; PTHR10584; SUGAR KINASE; 1.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR Pfam; PF00294; PfkB; 1.
DR PRINTS; PR00990; RIBOKINASE.
DR SUPFAM; SSF53613; Ribokinase-like; 1.
DR SUPFAM; SSF51658; Xylose isomerase-like; 1.
DR PROSITE; PS51415; XYLOSE_ISOMERASE; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_03215};
KW Carbohydrate metabolism {ECO:0000256|ARBA:ARBA00023277, ECO:0000256|HAMAP-
KW Rule:MF_03215};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_03215};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000313|EMBL:GBF87518.1};
KW Kinase {ECO:0000256|HAMAP-Rule:MF_03215, ECO:0000313|EMBL:GBF87518.1};
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:UP000247498};
KW Signal {ECO:0000256|SAM:SignalP};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_03215}.
FT SIGNAL 1..25
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 26..794
FT /note="Ribokinase"
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5015989710"
FT DOMAIN 43..354
FT /note="Carbohydrate kinase PfkB"
FT /evidence="ECO:0000259|Pfam:PF00294"
FT DOMAIN 498..724
FT /note="Xylose isomerase-like TIM barrel"
FT /evidence="ECO:0000259|Pfam:PF01261"
FT REGION 280..300
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 364..416
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 368..383
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 310
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 49..51
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 79..83
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 187
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 232
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 268..273
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 304
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 306
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 309..310
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 310
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 341
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 344
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 346
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
FT BINDING 350
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03215"
SQ SEQUENCE 794 AA; 79233 MW; 6BC15D2F67F415F7 CRC64;
MPGIRDHALP QLLALVPVLL LLGAAAPRAP TAAAAAVTPP PLLVVGSLNA DTTILLDRLP
ARGECLQSIR PVPSMAVGGK GANQAVAAAR LRAPGAPPPR FACRFGDDGP GKWMESELRR
EGLDLSLAAA APGVPSGSGI VWLDAGGAAT SVVLGGANTE GWGGAAALAA AAAAAVRGAG
ALLLQREVPE AVNAAFASAA AAAGVPVLLD AGGVDAPAGR ELLAGADYFA PNELELQRLT
GLPTASLAQA HAAARSLVDA GARRVLVTLG ERGALLIDAS RGAGEEPEET RQPPLPVPGG
AVVDATAAGD AFRAAFAVAL AQEGRTPREA LRFAAAAGAL AVARAGAMPS LPTRAEVEAL
LAAHPASEDG DSNSSSSGGG GGGDDSSEAQ GAAGASARGT EVARPPRARG AAAGGGTCPG
APGAGGGTCP GGGAPPGASA ERCPLRFASR LNSMRARREL VEGSPGDAAR DDVIGWIARQ
GRVRGLGAVY FNHPQHTEGR TPQQLLAALA SAGLAAAGVA LRFPEAFRAG AFTNPDADAR
AAALALAADG CRWARELGAD EVVVWSAFDG YDYHLQADYG AAWSRAVEGL RALADACPGV
EVALEWKPTD PASRFSFVPS TGAALLLARQ VNRTNFGLTL DTGHMLMAGE NSAQSVALAA
AEGRLFGVHL NDGHSRVGAE DGLVFGSVHS SAALELVYWL RRVGFDGTVY FDTFPSNEDP
VREAELNVRR FKALWARAAA LDAAGAADHL ARHDALGAME VADAAEAAAA GAGAGAGGEG
CGCGCGGGGA GEEV
//
