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Ribokinase (RK) (EC 2.7.1.15)

 A0A0M0QD28_SALCE        Unreviewed;       404 AA.
A0A0M0QD28;
11-NOV-2015, integrated into UniProtKB/TrEMBL.
11-NOV-2015, sequence version 1.
05-DEC-2018, entry version 35.
RecName: Full=Ribokinase {ECO:0000256|HAMAP-Rule:MF_01987};
Short=RK {ECO:0000256|HAMAP-Rule:MF_01987};
EC=2.7.1.15 {ECO:0000256|HAMAP-Rule:MF_01987};
Name=rbsK_2 {ECO:0000313|EMBL:SUE63930.1};
Synonyms=rbsK {ECO:0000256|HAMAP-Rule:MF_01987},
rbsK_3 {ECO:0000313|EMBL:GAR74872.1};
ORFNames=A7S24_15825 {ECO:0000313|EMBL:OHI62672.1},
A7S72_18125 {ECO:0000313|EMBL:OHK36857.1},
AIV63_08935 {ECO:0000313|EMBL:PXQ56965.1},
BUJ17_0009675 {ECO:0000313|EMBL:RII47300.1},
BUJ19_020960 {ECO:0000313|EMBL:PUU02986.1},
CBI64_15605 {ECO:0000313|EMBL:PEH24304.1},
CHE19_01605 {ECO:0000313|EMBL:AXD17399.1},
IN69_01620 {ECO:0000313|EMBL:KTO49731.1},
IN77_06125 {ECO:0000313|EMBL:KTO86468.1},
IN95_07150 {ECO:0000313|EMBL:KTP68728.1},
NCTC6022_00427 {ECO:0000313|EMBL:SUE63930.1},
NCTC6385_00348 {ECO:0000313|EMBL:SUF93511.1},
NGUA18_02777 {ECO:0000313|EMBL:GAR74872.1};
Salmonella choleraesuis.
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Salmonella.
NCBI_TaxID=28901 {ECO:0000313|EMBL:KTP68728.1, ECO:0000313|Proteomes:UP000053698};
[1] {ECO:0000313|Proteomes:UP000053698, ECO:0000313|Proteomes:UP000053981, ECO:0000313|Proteomes:UP000054402}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=CVM 43802 {ECO:0000313|EMBL:KTO49731.1,
ECO:0000313|Proteomes:UP000054402},
CVM 43810 {ECO:0000313|EMBL:KTO86468.1,
ECO:0000313|Proteomes:UP000053981}, and
CVM 43828 {ECO:0000313|EMBL:KTP68728.1,
ECO:0000313|Proteomes:UP000053698};
Chen Y., Folster J., Ayers S., Kabera C., Li C., Mukherjee S., Lam C.,
Zhao S., McDermott P.;
"Salmonella Genotype and Phenotype Association.";
Submitted (SEP-2014) to the EMBL/GenBank/DDBJ databases.
[2] {ECO:0000313|EMBL:GAR74872.1, ECO:0000313|Proteomes:UP000069392}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=NGUA18 {ECO:0000313|EMBL:GAR74872.1,
ECO:0000313|Proteomes:UP000069392};
Useh N.M., Ngbede E.O., Akange N., Thomas M., Foley A., Keena M.C.,
Nelson E., Christopher-Hennings J., Tomita M., Suzuki H., Scaria J.;
"Draft Genome Sequences of 37 Salmonella enterica Strains Isolated
from Poultry Sources in Nigeria.";
Genome Announc. 4:e00315-16(2016).
[3] {ECO:0000313|Proteomes:UP000069392}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=NGUA18 {ECO:0000313|Proteomes:UP000069392};
Useh N.M., Scaria J., Suzuki H.;
"Salmonella enterica strains from poultry sources in Nigeria, whole
genome shotgun sequence.";
Submitted (JAN-2016) to the EMBL/GenBank/DDBJ databases.
[4] {ECO:0000313|EMBL:GAR74872.1}
NUCLEOTIDE SEQUENCE.
STRAIN=NGUA18 {ECO:0000313|EMBL:GAR74872.1};
Oliw E.H.;
Submitted (JAN-2016) to the EMBL/GenBank/DDBJ databases.
[5] {ECO:0000313|EMBL:OHI62672.1, ECO:0000313|Proteomes:UP000179591, ECO:0000313|Proteomes:UP000180071}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=CFSAN044902 {ECO:0000313|EMBL:OHI62672.1,
ECO:0000313|Proteomes:UP000179591}, and
CFSAN044950 {ECO:0000313|EMBL:OHK36857.1,
ECO:0000313|Proteomes:UP000180071};
Bell R.;
"Whole genome sequencing of Salmonella enterica.";
Submitted (SEP-2016) to the EMBL/GenBank/DDBJ databases.
[6] {ECO:0000313|EMBL:PUU02986.1, ECO:0000313|Proteomes:UP000215575, ECO:0000313|Proteomes:UP000245285}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=CFSAN051021 {ECO:0000313|EMBL:RII47300.1,
ECO:0000313|Proteomes:UP000245285}, and
CFSAN051023 {ECO:0000313|EMBL:PUU02986.1,
ECO:0000313|Proteomes:UP000215575};
Sun Z.S., Albrecht U., Echele G., Lee C.C.;
Submitted (JUL-2017) to the EMBL/GenBank/DDBJ databases.
[7] {ECO:0000313|EMBL:PEH24304.1, ECO:0000313|Proteomes:UP000219891}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=CFSAN064288 {ECO:0000313|EMBL:PEH24304.1,
ECO:0000313|Proteomes:UP000219891};
Bell R., Levy K.;
"Whole genome sequencing of Salmonella enterica.";
Submitted (AUG-2017) to the EMBL/GenBank/DDBJ databases.
[8] {ECO:0000313|EMBL:PUU02986.1, ECO:0000313|Proteomes:UP000215575}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=CFSAN051023 {ECO:0000313|EMBL:PUU02986.1,
ECO:0000313|Proteomes:UP000215575};
Bell R.;
"Whole genome sequencing of Salmonella enterica.";
Submitted (APR-2018) to the EMBL/GenBank/DDBJ databases.
[9] {ECO:0000313|EMBL:PXQ56965.1, ECO:0000313|Proteomes:UP000247911}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=CFSAN035740 {ECO:0000313|EMBL:PXQ56965.1,
ECO:0000313|Proteomes:UP000247911};
Bell R.;
"Whole genome sequencing of Salmonella enterica serotype newport.";
Submitted (MAY-2018) to the EMBL/GenBank/DDBJ databases.
[10] {ECO:0000313|EMBL:AXD17399.1, ECO:0000313|Proteomes:UP000252033}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=SA20094620 {ECO:0000313|EMBL:AXD17399.1,
ECO:0000313|Proteomes:UP000252033};
Nash J.H.E., Robertson J., Bessonov K.;
"Completed Genome Sequences of 32 Strains from Various Serotypes of
Salmonella enterica.";
Submitted (JUN-2018) to the EMBL/GenBank/DDBJ databases.
[11] {ECO:0000313|EMBL:SUE63930.1, ECO:0000313|Proteomes:UP000254463, ECO:0000313|Proteomes:UP000255455}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=NCTC6022 {ECO:0000313|EMBL:SUE63930.1,
ECO:0000313|Proteomes:UP000255455}, and
NCTC6385 {ECO:0000313|EMBL:SUF93511.1,
ECO:0000313|Proteomes:UP000254463};
Pathogen Informatics;
Doyle S.;
Submitted (JUN-2018) to the EMBL/GenBank/DDBJ databases.
[12] {ECO:0000313|EMBL:RII47300.1, ECO:0000313|Proteomes:UP000245285}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=CFSAN051021 {ECO:0000313|EMBL:RII47300.1,
ECO:0000313|Proteomes:UP000245285};
Bell R.;
"Whole genome sequencing of Salmonella enterica.";
Submitted (AUG-2018) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: Catalyzes the phosphorylation of ribose at O-5 in a
reaction requiring ATP and magnesium. The resulting D-ribose-5-
phosphate can then be used either for sythesis of nucleotides,
histidine, and tryptophan, or as a component of the pentose
phosphate pathway. {ECO:0000256|HAMAP-Rule:MF_01987}.
-!- CATALYTIC ACTIVITY:
Reaction=ATP + D-ribose = ADP + D-ribose 5-phosphate + H(+);
Xref=Rhea:RHEA:13697, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
ChEBI:CHEBI:47013, ChEBI:CHEBI:78346, ChEBI:CHEBI:456216;
EC=2.7.1.15; Evidence={ECO:0000256|HAMAP-Rule:MF_01987};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000256|HAMAP-Rule:MF_01987};
Note=Requires a divalent cation, most likely magnesium in vivo, as
an electrophilic catalyst to aid phosphoryl group transfer. It is
the chelate of the metal and the nucleotide that is the actual
substrate. {ECO:0000256|HAMAP-Rule:MF_01987};
-!- ACTIVITY REGULATION: Activated by a monovalent cation that binds
near, but not in, the active site. The most likely occupant of the
site in vivo is potassium. Ion binding induces a conformational
change that may alter substrate affinity. {ECO:0000256|HAMAP-
Rule:MF_01987}.
-!- PATHWAY: Carbohydrate metabolism; D-ribose degradation; D-ribose
5-phosphate from beta-D-ribopyranose: step 2/2.
{ECO:0000256|HAMAP-Rule:MF_01987}.
-!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_01987}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01987}.
-!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family.
Ribokinase subfamily. {ECO:0000256|HAMAP-Rule:MF_01987}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation
of feature annotation. {ECO:0000256|HAMAP-Rule:MF_01987}.
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EMBL; CP030185; AXD17399.1; -; Genomic_DNA.
EMBL; BCOQ01000249; GAR74872.1; -; Genomic_DNA.
EMBL; JYRT01000005; KTO49731.1; -; Genomic_DNA.
EMBL; JYSB01000015; KTO86468.1; -; Genomic_DNA.
EMBL; JYST01000013; KTP68728.1; -; Genomic_DNA.
EMBL; MLSL01000007; OHI62672.1; -; Genomic_DNA.
EMBL; MLTX01000007; OHK36857.1; -; Genomic_DNA.
EMBL; NPOC01000006; PEH24304.1; -; Genomic_DNA.
EMBL; NLBR02000010; PUU02986.1; -; Genomic_DNA.
EMBL; QJCJ01000004; PXQ56965.1; -; Genomic_DNA.
EMBL; NMUD03000004; RII47300.1; -; Genomic_DNA.
EMBL; UGVT01000003; SUE63930.1; -; Genomic_DNA.
EMBL; UGWV01000002; SUF93511.1; -; Genomic_DNA.
RefSeq; WP_000667440.1; NZ_UGWT01000001.1.
EnsemblBacteria; GAR74872; GAR74872; NGUA18_02777.
EnsemblBacteria; KOP01240; KOP01240; AL032_18660.
EnsemblBacteria; KTM88498; KTM88498; IN36_15245.
EnsemblBacteria; KTO49731; KTO49731; IN69_01620.
EnsemblBacteria; KTP68728; KTP68728; IN95_07150.
EnsemblBacteria; OAG52149; OAG52149; A6C39_18130.
PATRIC; fig|28901.1106.peg.313; -.
UniPathway; UPA00916; UER00889.
Proteomes; UP000053698; Unassembled WGS sequence.
Proteomes; UP000053981; Unassembled WGS sequence.
Proteomes; UP000054402; Unassembled WGS sequence.
Proteomes; UP000069392; Unassembled WGS sequence.
Proteomes; UP000179591; Unassembled WGS sequence.
Proteomes; UP000180071; Unassembled WGS sequence.
Proteomes; UP000215575; Unassembled WGS sequence.
Proteomes; UP000219891; Unassembled WGS sequence.
Proteomes; UP000245285; Unassembled WGS sequence.
Proteomes; UP000247911; Unassembled WGS sequence.
Proteomes; UP000252033; Chromosome.
Proteomes; UP000254463; Unassembled WGS sequence.
Proteomes; UP000255455; Unassembled WGS sequence.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004747; F:ribokinase activity; IEA:UniProtKB-UniRule.
GO; GO:0019303; P:D-ribose catabolic process; IEA:UniProtKB-UniRule.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-UniRule.
CDD; cd01174; ribokinase; 1.
Gene3D; 1.10.10.10; -; 1.
Gene3D; 3.40.1190.20; -; 1.
HAMAP; MF_01987; Ribokinase; 1.
InterPro; IPR002173; Carboh/pur_kinase_PfkB_CS.
InterPro; IPR011877; D_ribokin.
InterPro; IPR001034; DeoR_HTH.
InterPro; IPR011611; PfkB_dom.
InterPro; IPR002139; Ribo/fructo_kinase.
InterPro; IPR029056; Ribokinase-like.
InterPro; IPR036388; WH-like_DNA-bd_sf.
InterPro; IPR036390; WH_DNA-bd_sf.
Pfam; PF08220; HTH_DeoR; 1.
Pfam; PF00294; PfkB; 1.
PRINTS; PR00037; HTHLACR.
PRINTS; PR00990; RIBOKINASE.
SMART; SM00420; HTH_DEOR; 1.
SUPFAM; SSF46785; SSF46785; 1.
SUPFAM; SSF53613; SSF53613; 1.
PROSITE; PS51000; HTH_DEOR_2; 1.
PROSITE; PS00584; PFKB_KINASES_2; 1.
3: Inferred from homology;
ATP-binding {ECO:0000256|HAMAP-Rule:MF_01987};
Carbohydrate metabolism {ECO:0000256|HAMAP-Rule:MF_01987};
Coiled coil {ECO:0000256|SAM:Coils};
Complete proteome {ECO:0000313|Proteomes:UP000053698,
ECO:0000313|Proteomes:UP000053981, ECO:0000313|Proteomes:UP000054402,
ECO:0000313|Proteomes:UP000069392};
Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01987};
DNA-binding {ECO:0000256|SAAS:SAAS01006767};
Kinase {ECO:0000256|HAMAP-Rule:MF_01987,
ECO:0000256|RuleBase:RU003704, ECO:0000256|SAAS:SAAS00061343,
ECO:0000313|EMBL:KTP68728.1};
Magnesium {ECO:0000256|HAMAP-Rule:MF_01987};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_01987};
Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01987};
Potassium {ECO:0000256|HAMAP-Rule:MF_01987};
Transcription {ECO:0000256|SAAS:SAAS01006775};
Transcription regulation {ECO:0000256|SAAS:SAAS01006775};
Transferase {ECO:0000256|HAMAP-Rule:MF_01987,
ECO:0000256|RuleBase:RU003704, ECO:0000256|SAAS:SAAS00061343,
ECO:0000313|EMBL:KTP68728.1}.
DOMAIN 2 57 HTH deoR-type.
{ECO:0000259|PROSITE:PS51000}.
NP_BIND 311 316 ATP. {ECO:0000256|HAMAP-Rule:MF_01987}.
NP_BIND 342 343 ATP. {ECO:0000256|HAMAP-Rule:MF_01987}.
REGION 101 103 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_01987}.
REGION 129 133 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_01987}.
COILED 227 247 {ECO:0000256|SAM:Coils}.
ACT_SITE 343 343 Proton acceptor. {ECO:0000256|HAMAP-
Rule:MF_01987}.
METAL 337 337 Potassium. {ECO:0000256|HAMAP-
Rule:MF_01987}.
METAL 339 339 Potassium; via carbonyl oxygen.
{ECO:0000256|HAMAP-Rule:MF_01987}.
METAL 373 373 Potassium; via carbonyl oxygen.
{ECO:0000256|HAMAP-Rule:MF_01987}.
METAL 376 376 Potassium; via carbonyl oxygen.
{ECO:0000256|HAMAP-Rule:MF_01987}.
BINDING 231 231 Substrate. {ECO:0000256|HAMAP-
Rule:MF_01987}.
BINDING 275 275 ATP. {ECO:0000256|HAMAP-Rule:MF_01987}.
BINDING 343 343 Substrate. {ECO:0000256|HAMAP-
Rule:MF_01987}.
SEQUENCE 404 AA; 43466 MW; E7BF9236BFD63EEC CRC64;
MKFERHHRIL KELSISGVVK VSNLAKSLKV TKETIRSDLN ELAGQGYLTR CHGGAFITLD
SLDNVAKNEI AYVLEKYESA QKIKKGLSAM KNNVCVIGSF NVDIISYLPR LPSTGESLLA
DKFIFSPGGK GCNQALAASY ADSDVHFITK VGSDHFSDYA INFINSSKIH KSVIYQTKET
QTGTATIMVN GDTGDNVIAI YPGANMTISP DEITIQKEAI VHSDIVLVQL ETNYEALQQT
IRLAQKNDIP VIINPAPYND MVNTIIDNID YITPNETEAG LLANMAVNDI ESAKCAAKII
HQKGVKNTII TLGSKGSLAY DGTQFIYSPA FPAVVKNTAG AGDAFNGALA SGLAKGKSLA
SALCYASAFA SLAVETPNAS DMPENDSVLH RIQGSHYKQT ISTH


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