ID RBSK_ARATH Reviewed; 379 AA.
AC A1A6H3; Q9SHH5;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 24-JAN-2024, entry version 130.
DE RecName: Full=Ribokinase {ECO:0000255|HAMAP-Rule:MF_03215};
DE Short=AtRBSK {ECO:0000303|PubMed:27601466};
DE Short=RK {ECO:0000255|HAMAP-Rule:MF_03215};
DE EC=2.7.1.15 {ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000269|PubMed:27601466};
DE Flags: Precursor;
GN Name=RBSK {ECO:0000303|PubMed:27601466};
GN OrderedLocusNames=At1g17160 {ECO:0000312|Araport:AT1G17160};
GN ORFNames=F20D23.14 {ECO:0000312|EMBL:AAD50017.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Bautista V.R., Kim C.J., Chen H., Quinitio C., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF 1-MET--VAL-74, CATALYTIC
RP ACTIVITY, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY
RP REGULATION.
RC STRAIN=cv. Columbia;
RX PubMed=27601466; DOI=10.1074/jbc.m116.754689;
RA Riggs J.W., Rockwell N.C., Cavales P.C., Callis J.;
RT "Identification of the plant ribokinase and discovery of a role for
RT Arabidopsis ribokinase in nucleoside metabolism.";
RL J. Biol. Chem. 291:22572-22582(2016).
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 (By
CC similarity) (PubMed:27601466). Can also use xylose and fructose as
CC carbohydrate substrates with a low efficiency (PubMed:27601466). Can
CC use GTP, and, to a lower extent, CTP and UTP as alternative phosphoryl
CC donors (PubMed:27601466). {ECO:0000255|HAMAP-Rule:MF_03215,
CC ECO:0000269|PubMed:27601466}.
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:27601466};
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 (By similarity) (PubMed:27601466). Repressed
CC by calcium, rubidium and sodium (PubMed:27601466). Substrate inhibition
CC is observed in the presence of high ATP concentration (Ki=2.44 mM)
CC (PubMed:27601466). {ECO:0000255|HAMAP-Rule:MF_03215,
CC ECO:0000269|PubMed:27601466}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=150 uM for D-ribose {ECO:0000269|PubMed:27601466};
CC KM=45 uM for ATP {ECO:0000269|PubMed:27601466};
CC Note=kcat is 2 sec(-1). {ECO:0000269|PubMed:27601466};
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}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_03215}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma, chloroplast nucleoid
CC {ECO:0000269|PubMed:27601466}.
CC -!- DISRUPTION PHENOTYPE: Abnormal accumulation of D-ribose. D-ribose
CC hypersensitivity; normal growth except in the presence of D-ribose,
CC which leads to chlorosis and growth inhibition.
CC {ECO:0000269|PubMed:27601466}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family. Ribokinase
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_03215}.
CC -!- CAUTION: Cleavage site of the transit peptide is likely localized
CC before the predicted cleavage site at Val-74, probably around His-67.
CC {ECO:0000305|PubMed:27601466}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD50017.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC007651; AAD50017.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002684; AEE29552.1; -; Genomic_DNA.
DR EMBL; BT029492; ABL66749.1; -; mRNA.
DR PIR; F86307; F86307.
DR RefSeq; NP_173159.1; NM_101577.5.
DR PDB; 6ILR; X-ray; 1.97 A; A/B=68-379.
DR PDB; 6ILS; X-ray; 1.80 A; A/B=68-379.
DR PDB; 6ILT; X-ray; 2.20 A; A/B=68-379.
DR PDBsum; 6ILR; -.
DR PDBsum; 6ILS; -.
DR PDBsum; 6ILT; -.
DR AlphaFoldDB; A1A6H3; -.
DR SMR; A1A6H3; -.
DR STRING; 3702.A1A6H3; -.
DR PaxDb; 3702-AT1G17160-1; -.
DR ProteomicsDB; 181456; -.
DR EnsemblPlants; AT1G17160.1; AT1G17160.1; AT1G17160.
DR GeneID; 838287; -.
DR Gramene; AT1G17160.1; AT1G17160.1; AT1G17160.
DR KEGG; ath:AT1G17160; -.
DR Araport; AT1G17160; -.
DR TAIR; AT1G17160; RBSK.
DR eggNOG; KOG2855; Eukaryota.
DR HOGENOM; CLU_027634_2_2_1; -.
DR InParanoid; A1A6H3; -.
DR OMA; DIVLIQQ; -.
DR OrthoDB; 324851at2759; -.
DR PhylomeDB; A1A6H3; -.
DR BioCyc; ARA:AT1G17160-MONOMER; -.
DR BioCyc; MetaCyc:AT1G17160-MONOMER; -.
DR BRENDA; 2.7.1.15; 399.
DR UniPathway; UPA00916; UER00889.
DR PRO; PR:A1A6H3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; A1A6H3; baseline and differential.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0042644; C:chloroplast nucleoid; IEA:UniProtKB-SubCell.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-UniRule.
DR GO; GO:0042646; C:plastid nucleoid; IDA:TAIR.
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:TAIR.
DR GO; GO:0019303; P:D-ribose catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009116; P:nucleoside metabolic process; IGI:TAIR.
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 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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Carbohydrate metabolism; Chloroplast; Kinase;
KW Magnesium; Metal-binding; Nucleotide-binding; Plastid; Potassium;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast"
FT /evidence="ECO:0000305|PubMed:27601466"
FT CHAIN ?..379
FT /note="Ribokinase"
FT /id="PRO_0000446983"
FT ACT_SITE 325
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 78..80
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 106..110
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 210
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 255
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 291..296
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 319
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 321
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 324..325
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 325
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 355
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 358
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 360
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 364
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT MUTAGEN 1..74
FT /note="Missing: Loss of ribokinase activity."
FT /evidence="ECO:0000269|PubMed:27601466"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 78..87
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 98..105
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 107..117
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 122..125
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 127..131
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 132..141
FT /evidence="ECO:0007829|PDB:6ILS"
FT TURN 143..146
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 154..159
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 162..169
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 170..172
FT /evidence="ECO:0007829|PDB:6ILR"
FT STRAND 174..179
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 182..185
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 193..200
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 203..211
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 213..226
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 230..236
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 243..246
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 250..253
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 256..263
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 270..283
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 286..291
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 297..301
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 307..309
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 323..336
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 341..356
FT /evidence="ECO:0007829|PDB:6ILS"
FT STRAND 358..361
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 362..364
FT /evidence="ECO:0007829|PDB:6ILS"
FT HELIX 368..376
FT /evidence="ECO:0007829|PDB:6ILS"
SQ SEQUENCE 379 AA; 40189 MW; 5EF5A99F01E3BF6D CRC64;
MMKGISSVSQ SINYNPYIEF NRPQLQISTV NPNPAQSRFS RPRSLRVLSL SADPSANRNP
KSAVDAHAPP LVVVGSANAD IYVEIERLPK EGETISAKTG QTLAGGKGAN QAACGAKLMY
PTYFVGRLGE DAHGKLIAEA LGDDGCGVHL DYVRSVNNEP TGHAVVMLQS DGQNSIIIVG
GANMKAWPEI MSDDDLEIVR NAGIVLLQRE IPDSINIQVA KAVKKAGVPV ILDVGGMDTP
IPNELLDSID ILSPNETELS RLTGMPTETF EQISQAVAKC HKLGVKQVLV KLGSKGSALF
IQGEKPIQQS IIPAAQVVDT TGAGDTFTAA FAVAMVEGKS HEECLRFAAA AASLCVQVKG
AIPSMPDRKS VLKLLKFSI
//
