RBSK_LEIMA
ID RBSK_LEIMA Reviewed; 329 AA.
AC E9AD19;
DT 13-APR-2016, integrated into UniProtKB/Swiss-Prot.
DT 05-APR-2011, sequence version 1.
DT 03-AUG-2022, entry version 63.
DE RecName: Full=Ribokinase {ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000303|PubMed:17558452};
DE Short=RK {ECO:0000255|HAMAP-Rule:MF_03215};
DE EC=2.7.1.15 {ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000269|PubMed:17558452};
GN ORFNames=LMJF_27_0420;
OS Leishmania major.
OC Eukaryota; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
OC Trypanosomatida; Trypanosomatidae; Leishmaniinae; Leishmania.
OX NCBI_TaxID=5664;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MHOM/IL/81/Friedlin;
RX PubMed=16020728; DOI=10.1126/science.1112680;
RA Ivens A.C., Peacock C.S., Worthey E.A., Murphy L., Aggarwal G.,
RA Berriman M., Sisk E., Rajandream M.A., Adlem E., Aert R., Anupama A.,
RA Apostolou Z., Attipoe P., Bason N., Bauser C., Beck A., Beverley S.M.,
RA Bianchettin G., Borzym K., Bothe G., Bruschi C.V., Collins M., Cadag E.,
RA Ciarloni L., Clayton C., Coulson R.M.R., Cronin A., Cruz A.K., Davies R.M.,
RA De Gaudenzi J., Dobson D.E., Duesterhoeft A., Fazelina G., Fosker N.,
RA Frasch A.C., Fraser A., Fuchs M., Gabel C., Goble A., Goffeau A.,
RA Harris D., Hertz-Fowler C., Hilbert H., Horn D., Huang Y., Klages S.,
RA Knights A., Kube M., Larke N., Litvin L., Lord A., Louie T., Marra M.,
RA Masuy D., Matthews K., Michaeli S., Mottram J.C., Mueller-Auer S.,
RA Munden H., Nelson S., Norbertczak H., Oliver K., O'neil S., Pentony M.,
RA Pohl T.M., Price C., Purnelle B., Quail M.A., Rabbinowitsch E.,
RA Reinhardt R., Rieger M., Rinta J., Robben J., Robertson L., Ruiz J.C.,
RA Rutter S., Saunders D., Schaefer M., Schein J., Schwartz D.C., Seeger K.,
RA Seyler A., Sharp S., Shin H., Sivam D., Squares R., Squares S., Tosato V.,
RA Vogt C., Volckaert G., Wambutt R., Warren T., Wedler H., Woodward J.,
RA Zhou S., Zimmermann W., Smith D.F., Blackwell J.M., Stuart K.D.,
RA Barrell B.G., Myler P.J.;
RT "The genome of the kinetoplastid parasite, Leishmania major.";
RL Science 309:436-442(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MHOM/IL/81/Friedlin;
RX PubMed=22038252; DOI=10.1101/gr.122945.111;
RA Rogers M.B., Hilley J.D., Dickens N.J., Wilkes J., Bates P.A.,
RA Depledge D.P., Harris D., Her Y., Herzyk P., Imamura H., Otto T.D.,
RA Sanders M., Seeger K., Dujardin J.C., Berriman M., Smith D.F.,
RA Hertz-Fowler C., Mottram J.C.;
RT "Chromosome and gene copy number variation allow major structural change
RT between species and strains of Leishmania.";
RL Genome Res. 21:2129-2142(2011).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RX PubMed=17558452; DOI=10.1111/j.1745-7270.2007.00298.x;
RA Ogbunude P.O., Lamour N., Barrett M.P.;
RT "Molecular cloning, expression and characterization of ribokinase of
RT Leishmania major.";
RL Acta Biochim. Biophys. Sin. 39:462-466(2007).
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 Specifically phosphorylates D-ribose. Fails to phosphorylate 4, 5 or 6
CC D-carbon sugars (erythrose, threose, xylulose, arabinose, fructose and
CC glucose). {ECO:0000255|HAMAP-Rule:MF_03215,
CC ECO:0000269|PubMed:17558452}.
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:0000255|HAMAP-Rule:MF_03215,
CC ECO:0000269|PubMed:17558452};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_03215}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.2 mM for ATP {ECO:0000269|PubMed:17558452};
CC KM=0.3 mM for ribose {ECO:0000269|PubMed:17558452};
CC Note=kcat is 10.2 sec(-1) with ATP as substrate and 10.8 sec(-1) with
CC ribose as substrate. {ECO:0000269|PubMed:17558452};
CC -!- PATHWAY: Carbohydrate metabolism; D-ribose degradation; D-ribose 5-
CC phosphate from beta-D-ribopyranose: step 2/2. {ECO:0000255|HAMAP-
CC Rule:MF_03215, ECO:0000305|PubMed:17558452}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_03215}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03215}.
CC Nucleus {ECO:0000255|HAMAP-Rule:MF_03215}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family. Ribokinase
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_03215}.
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DR EMBL; FR796423; CBZ12102.1; -; Genomic_DNA.
DR RefSeq; XP_003721848.1; XM_003721800.1.
DR AlphaFoldDB; E9AD19; -.
DR SMR; E9AD19; -.
DR STRING; 5664.LmjF.27.0420; -.
DR EnsemblProtists; CBZ12102; CBZ12102; LMJF_27_0420.
DR GeneID; 12982633; -.
DR KEGG; lma:LMJF_27_0420; -.
DR VEuPathDB; TriTrypDB:LmjF.27.0420; -.
DR VEuPathDB; TriTrypDB:LMJLV39_270009200; -.
DR VEuPathDB; TriTrypDB:LMJSD75_270009200; -.
DR eggNOG; KOG2855; Eukaryota.
DR HOGENOM; CLU_027634_2_3_1; -.
DR InParanoid; E9AD19; -.
DR OMA; TFCGYFA; -.
DR UniPathway; UPA00916; UER00889.
DR Proteomes; UP000000542; Chromosome 27.
DR GO; GO:0020015; C:glycosome; ISO:GeneDB.
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; IDA:GeneDB.
DR GO; GO:0019303; P:D-ribose catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006014; P:D-ribose metabolic process; IDA:GeneDB.
DR CDD; cd01174; ribokinase; 1.
DR Gene3D; 3.40.1190.20; -; 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 Pfam; PF00294; PfkB; 1.
DR PRINTS; PR00990; RIBOKINASE.
DR SUPFAM; SSF53613; SSF53613; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Carbohydrate metabolism; Cytoplasm; Kinase; Magnesium;
KW Metal-binding; Nucleotide-binding; Nucleus; Potassium; Reference proteome;
KW Transferase.
FT CHAIN 1..329
FT /note="Ribokinase"
FT /id="PRO_0000436026"
FT ACT_SITE 278
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 25..27
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 53..57
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 160
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 209
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 245..250
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 272
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 274
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 277..278
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 278
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 302
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 308
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 311
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 313
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 317
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
SQ SEQUENCE 329 AA; 35342 MW; FAD47833EFCEFE8E CRC64;
MHRVQNVQSH VGEYAPDILV VGSCFLDYVG YVDHMPQVGE TMHSESFHKG FGGKGANQAV
AAGRLGAKVA MVSMVGTDGD GSDYIKELER NGVHTAYMLR TGKSSTGLAM ILVDTKSSNN
EIVICPNATN YFTPELLRAQ TSNYEKILHT GLKYLICQNE IPLPTTLDTI KEAHSRGVYT
VFNSAPAPKP AEVEQIKPFL PYVSLFCPNE VEAALITGMK VTDTESAFRA IKALQQLGVR
DVVITLGAAG FALSENGAEP VHVTGKHVKA VDTTGAGDCF VGSMVYFMSR GRNLLEACKR
ANECAAISVT RKGTQLSYPH PSELPAGVT
