RBSK_STAAC
ID RBSK_STAAC Reviewed; 304 AA.
AC A0A0H2WZY4;
DT 18-SEP-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-SEP-2015, sequence version 1.
DT 03-AUG-2022, entry version 38.
DE RecName: Full=Ribokinase {ECO:0000255|HAMAP-Rule:MF_01987};
DE Short=RK {ECO:0000255|HAMAP-Rule:MF_01987};
DE EC=2.7.1.15 {ECO:0000255|HAMAP-Rule:MF_01987, ECO:0000269|PubMed:22198595};
GN Name=rbsK {ECO:0000255|HAMAP-Rule:MF_01987}; OrderedLocusNames=SACOL0253;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
RN [2] {ECO:0007744|PDB:3RY7}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS), FUNCTION, SUBUNIT, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY REGULATION.
RX PubMed=22198595; DOI=10.1016/j.jsb.2011.12.010;
RA Li J., Wang C., Wu Y., Wu M., Wang L., Wang Y., Zang J.;
RT "Crystal structure of Sa239 reveals the structural basis for the activation
RT of ribokinase by monovalent cations.";
RL J. Struct. Biol. 177:578-582(2012).
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:0000255|HAMAP-Rule:MF_01987, ECO:0000269|PubMed:22198595}.
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_01987,
CC ECO:0000269|PubMed:22198595};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01987};
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_01987};
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_01987,
CC ECO:0000269|PubMed:22198595}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.66 mM for ATP (in absence of K(+))
CC {ECO:0000269|PubMed:22198595};
CC KM=2.19 mM for ATP (in presence of 100 mM K(+))
CC {ECO:0000269|PubMed:22198595};
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_01987}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01987,
CC ECO:0000269|PubMed:22198595}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01987}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family. Ribokinase
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01987}.
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DR EMBL; CP000046; AAW38808.1; -; Genomic_DNA.
DR RefSeq; WP_000182751.1; NC_002951.2.
DR PDB; 3RY7; X-ray; 2.15 A; A=1-304.
DR PDBsum; 3RY7; -.
DR AlphaFoldDB; A0A0H2WZY4; -.
DR SMR; A0A0H2WZY4; -.
DR EnsemblBacteria; AAW38808; AAW38808; SACOL0253.
DR KEGG; sac:SACOL0253; -.
DR HOGENOM; CLU_027634_2_0_9; -.
DR OMA; AMDSIPF; -.
DR BRENDA; 2.7.1.15; 3352.
DR UniPathway; UPA00916; UER00889.
DR Proteomes; UP000000530; Chromosome.
DR GO; GO:0005737; C:cytoplasm; 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 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 Pfam; PF00294; PfkB; 1.
DR PRINTS; PR00990; RIBOKINASE.
DR SUPFAM; SSF53613; SSF53613; 1.
DR TIGRFAMs; TIGR02152; D_ribokin_bact; 1.
DR PROSITE; PS00584; PFKB_KINASES_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Carbohydrate metabolism; Cytoplasm; Kinase;
KW Magnesium; Metal-binding; Nucleotide-binding; Potassium; Transferase.
FT CHAIN 1..304
FT /note="Ribokinase"
FT /id="PRO_0000447879"
FT ACT_SITE 254
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 12..14
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 41..45
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 142
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 186
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 222..227
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 248
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 250
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 253..254
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 254
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 279
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 285
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 288
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 290
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT BINDING 294
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01987"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 12..18
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 42..52
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 62..66
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 95..101
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 114..118
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 121..125
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 128..132
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 145..157
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 161..165
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 174..177
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 181..183
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 187..194
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 201..213
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:3RY7"
FT STRAND 236..239
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 252..263
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 271..283
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 292..294
FT /evidence="ECO:0007829|PDB:3RY7"
FT HELIX 298..302
FT /evidence="ECO:0007829|PDB:3RY7"
SQ SEQUENCE 304 AA; 32449 MW; 1751615653A3BFC4 CRC64;
MTNKVVILGS TNVDQFLTVE RYAQPGETLH VEEAQKAFGG GKGANQAIAT ARMQADTTFI
TKIGTDGVAD FILEDFKVAH IDTSYIIKTA EAKTGQAFIT VNAEGQNTIY VYGGANMTMT
PEDVINAKDA IINADFVVAQ LEVPIPAIIS AFEIAKAHGV TTVLNPAPAK ALPNELLSLI
DIIVPNETEA ELLSGIKVTN EQSMKDNANY FLSIGIKTVL ITLGKQGTYF ATKNQSQHIE
AYKVNAIDTT AAGDTFIGAF VSRLNKSQDN LADAIDFGNK ASSLTVQKHG AQASIPLLEE
VNQV
