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Protein

Ribokinase

Gene

rbsK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation2 Publications

Catalytic activityi

ATP + D-ribose = ADP + D-ribose 5-phosphate.UniRule annotation3 Publications

Cofactori

Mg2+UniRule annotation1 Publication1 Publication, Mn2+1 PublicationNote: 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 (Probable). Also active with manganase (PubMed:16784868).UniRule annotation1 Publication1 Publication

Enzyme regulationi

Activated by a monovalent cation that binds near, but not in, the active site (PubMed:11786021). The most likely occupant of the site in vivo is potassium (PubMed:16784868, PubMed:11786021). Also activated by ammonium ion (PubMed:16784868). Ion binding induces a conformational change that may alter substrate affinity (Probable).UniRule annotation1 Publication2 Publications

Kineticsi

  1. KM=0.213 mM for ATP1 Publication
  2. KM=0.279 mM for D-ribose1 Publication
  3. KM=1.41 mM for 2-deoxy-D-ribose1 Publication
  4. KM=32 mM for D-arabinose1 Publication
  5. KM=31.6 mM for D-xylose1 Publication
  6. KM=8.2 mM for D-fructose1 Publication
  7. KM=0.65 mM for ribose (at pH 6.2 in the presence of 0 mM inorganic phosphate)1 Publication
  8. KM=0.43 mM for ribose (at pH 6.2 in the presence of 0.5 mM inorganic phosphate)1 Publication
  9. KM=0.27 mM for ribose (at pH 6.2 in the presence of 1 mM inorganic phosphate)1 Publication
  10. KM=0.23 mM for ribose (at pH 6.2 in the presence of 5 mM inorganic phosphate)1 Publication
  11. KM=0.21 mM for ribose (at pH 6.2 in the presence of 20 mM inorganic phosphate)1 Publication
  1. Vmax=122 µmol/min/mg enzyme toward ATP1 Publication
  2. Vmax=81 µmol/min/mg enzyme toward D-ribose1 Publication
  3. Vmax=25 µmol/min/mg enzyme toward 2-deoxy-D-ribose1 Publication
  4. Vmax=0.6 µmol/min/mg enzyme toward D-arabinose1 Publication
  5. Vmax=0.86 µmol/min/mg enzyme toward D-xylose1 Publication
  6. Vmax=0.226 µmol/min/mg enzyme toward D-fructose1 Publication
  7. Vmax=7.6 pmol/min/mg enzyme (at pH 6.2 in the presence of 0 mM inorganic phosphate)1 Publication
  8. Vmax=32.0 pmol/min/mg enzyme (at pH 6.2 in the presence of 0.5 mM inorganic phosphate)1 Publication
  9. Vmax=59.6 pmol/min/mg enzyme (at pH 6.2 in the presence of 1 mM inorganic phosphate)1 Publication
  10. Vmax=139.4 pmol/min/mg enzyme (at pH 6.2 in the presence of 5 mM inorganic phosphate)1 Publication
  11. Vmax=172.4 pmol/min/mg enzyme (at pH 6.2 in the presence of 20 mM inorganic phosphate)1 Publication

pH dependencei

Optimum pH is 8-9.1 Publication

Temperature dependencei

Optimum temperature is 30-50 degrees Celsius.1 Publication

Pathwayi: D-ribose degradation

This protein is involved in step 2 of the subpathway that synthesizes D-ribose 5-phosphate from beta-D-ribopyranose.UniRule annotation1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. D-ribose pyranase (rbsD)
  2. Ribokinase (rbsK)
This subpathway is part of the pathway D-ribose degradation, which is itself part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribose 5-phosphate from beta-D-ribopyranose, the pathway D-ribose degradation and in Carbohydrate metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei143 – 1431SubstrateUniRule annotation3 Publications
Binding sitei187 – 1871ATPUniRule annotation3 Publications
Metal bindingi249 – 2491PotassiumUniRule annotation1 Publication
Metal bindingi251 – 2511Potassium; via carbonyl oxygenUniRule annotation1 Publication
Active sitei255 – 2551Proton acceptorUniRule annotation1 Publication
Binding sitei255 – 2551SubstrateUniRule annotation3 Publications
Binding sitei279 – 2791ATPUniRule annotation3 Publications
Metal bindingi285 – 2851Potassium; via carbonyl oxygenUniRule annotation1 Publication
Metal bindingi288 – 2881Potassium; via carbonyl oxygenUniRule annotation1 Publication
Metal bindingi290 – 2901Potassium; via carbonyl oxygenUniRule annotation1 Publication
Metal bindingi294 – 2941PotassiumUniRule annotation1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi223 – 2286ATPUniRule annotation3 Publications
Nucleotide bindingi254 – 2552ATPUniRule annotation2 Publications

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • ribokinase activity Source: EcoCyc

GO - Biological processi

  • D-ribose catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Potassium

Enzyme and pathway databases

BioCyciEcoCyc:RIBOKIN-MONOMER.
ECOL316407:JW3731-MONOMER.
MetaCyc:RIBOKIN-MONOMER.
RETL1328306-WGS:GSTH-416-MONOMER.
RETL1328306-WGS:GSTH-5050-MONOMER.
BRENDAi2.7.1.15. 2026.
UniPathwayiUPA00916; UER00889.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribokinase1 PublicationUniRule annotation (EC:2.7.1.15UniRule annotation2 Publications)
Short name:
RKUniRule annotation
Gene namesi
Name:rbsK1 PublicationUniRule annotation
Ordered Locus Names:b3752, JW3731
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10818. rbsK.

Subcellular locationi

  • Cytoplasm UniRule annotationCurated

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL5093.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 309309RibokinasePRO_0000080097Add
BLAST

Proteomic databases

EPDiP0A9J6.
PaxDbiP0A9J6.
PRIDEiP0A9J6.

Interactioni

Subunit structurei

Homodimer.UniRule annotation1 Publication

Protein-protein interaction databases

BioGridi4259582. 11 interactions.
DIPiDIP-36178N.
IntActiP0A9J6. 3 interactions.
MINTiMINT-1321131.
STRINGi511145.b3752.

Chemistry

BindingDBiP0A9J6.

Structurei

Secondary structure

1
309
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 105Combined sources
Beta strandi14 – 207Combined sources
Beta strandi30 – 323Combined sources
Beta strandi36 – 416Combined sources
Helixi43 – 5412Combined sources
Beta strandi57 – 6711Combined sources
Helixi70 – 789Combined sources
Turni79 – 813Combined sources
Beta strandi87 – 904Combined sources
Beta strandi96 – 1027Combined sources
Beta strandi108 – 1136Combined sources
Helixi115 – 1195Combined sources
Helixi122 – 1265Combined sources
Helixi129 – 1346Combined sources
Beta strandi136 – 1405Combined sources
Beta strandi142 – 1443Combined sources
Helixi146 – 15813Combined sources
Beta strandi162 – 1654Combined sources
Helixi175 – 1784Combined sources
Beta strandi182 – 1843Combined sources
Helixi188 – 1958Combined sources
Helixi202 – 21413Combined sources
Beta strandi218 – 2236Combined sources
Helixi225 – 2273Combined sources
Beta strandi229 – 2335Combined sources
Beta strandi236 – 2405Combined sources
Helixi253 – 26614Combined sources
Helixi271 – 28616Combined sources
Beta strandi288 – 2914Combined sources
Helixi292 – 2943Combined sources
Helixi298 – 3069Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GQTX-ray2.34A/B/C/D1-309[»]
1RK2X-ray2.25A/B/C/D1-309[»]
1RKAX-ray2.30A1-309[»]
1RKDX-ray1.84A1-309[»]
1RKSX-ray2.40A1-309[»]
ProteinModelPortaliP0A9J6.
SMRiP0A9J6. Positions 2-308.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A9J6.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 163Substrate bindingUniRule annotation3 Publications
Regioni42 – 465Substrate bindingUniRule annotation3 Publications

Sequence similaritiesi

Belongs to the carbohydrate kinase PfkB family. Ribokinase subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108RVA. Bacteria.
COG0524. LUCA.
HOGENOMiHOG000235950.
InParanoidiP0A9J6.
KOiK00852.
OMAiNADHVIS.
OrthoDBiEOG64JFMD.
PhylomeDBiP0A9J6.

Family and domain databases

Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01987. Ribokinase.
InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
IPR011877. D_ribokin.
IPR011611. PfkB_dom.
IPR002139. Ribo/fructo_kinase.
IPR029056. Ribokinase-like.
[Graphical view]
PfamiPF00294. PfkB. 1 hit.
[Graphical view]
PRINTSiPR00990. RIBOKINASE.
SUPFAMiSSF53613. SSF53613. 1 hit.
TIGRFAMsiTIGR02152. D_ribokin_bact. 1 hit.
PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A9J6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQNAGSLVVL GSINADHILN LQSFPTPGET VTGNHYQVAF GGKGANQAVA
60 70 80 90 100
AGRSGANIAF IACTGDDSIG ESVRQQLATD NIDITPVSVI KGESTGVALI
110 120 130 140 150
FVNGEGENVI GIHAGANAAL SPALVEAQRE RIANASALLM QLESPLESVM
160 170 180 190 200
AAAKIAHQNK TIVALNPAPA RELPDELLAL VDIITPNETE AEKLTGIRVE
210 220 230 240 250
NDEDAAKAAQ VLHEKGIRTV LITLGSRGVW ASVNGEGQRV PGFRVQAVDT
260 270 280 290 300
IAAGDTFNGA LITALLEEKP LPEAIRFAHA AAAIAVTRKG AQPSVPWREE

IDAFLDRQR
Length:309
Mass (Da):32,291
Last modified:August 13, 1987 - v1
Checksum:i753729B41E64060E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13169 Genomic DNA. Translation: AAA51476.1.
L10328 Genomic DNA. Translation: AAA62105.1.
U00096 Genomic DNA. Translation: AAC76775.1.
AP009048 Genomic DNA. Translation: BAE77536.1.
PIRiA26305. KIECRB.
RefSeqiNP_418208.1. NC_000913.3.
WP_001300603.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76775; AAC76775; b3752.
BAE77536; BAE77536; BAE77536.
GeneIDi948260.
KEGGiecj:JW3731.
eco:b3752.
PATRICi32123003. VBIEscCol129921_3877.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13169 Genomic DNA. Translation: AAA51476.1.
L10328 Genomic DNA. Translation: AAA62105.1.
U00096 Genomic DNA. Translation: AAC76775.1.
AP009048 Genomic DNA. Translation: BAE77536.1.
PIRiA26305. KIECRB.
RefSeqiNP_418208.1. NC_000913.3.
WP_001300603.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GQTX-ray2.34A/B/C/D1-309[»]
1RK2X-ray2.25A/B/C/D1-309[»]
1RKAX-ray2.30A1-309[»]
1RKDX-ray1.84A1-309[»]
1RKSX-ray2.40A1-309[»]
ProteinModelPortaliP0A9J6.
SMRiP0A9J6. Positions 2-308.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259582. 11 interactions.
DIPiDIP-36178N.
IntActiP0A9J6. 3 interactions.
MINTiMINT-1321131.
STRINGi511145.b3752.

Chemistry

BindingDBiP0A9J6.
ChEMBLiCHEMBL5093.

Proteomic databases

EPDiP0A9J6.
PaxDbiP0A9J6.
PRIDEiP0A9J6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76775; AAC76775; b3752.
BAE77536; BAE77536; BAE77536.
GeneIDi948260.
KEGGiecj:JW3731.
eco:b3752.
PATRICi32123003. VBIEscCol129921_3877.

Organism-specific databases

EchoBASEiEB0811.
EcoGeneiEG10818. rbsK.

Phylogenomic databases

eggNOGiENOG4108RVA. Bacteria.
COG0524. LUCA.
HOGENOMiHOG000235950.
InParanoidiP0A9J6.
KOiK00852.
OMAiNADHVIS.
OrthoDBiEOG64JFMD.
PhylomeDBiP0A9J6.

Enzyme and pathway databases

UniPathwayiUPA00916; UER00889.
BioCyciEcoCyc:RIBOKIN-MONOMER.
ECOL316407:JW3731-MONOMER.
MetaCyc:RIBOKIN-MONOMER.
RETL1328306-WGS:GSTH-416-MONOMER.
RETL1328306-WGS:GSTH-5050-MONOMER.
BRENDAi2.7.1.15. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A9J6.
PROiP0A9J6.

Family and domain databases

Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01987. Ribokinase.
InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
IPR011877. D_ribokin.
IPR011611. PfkB_dom.
IPR002139. Ribo/fructo_kinase.
IPR029056. Ribokinase-like.
[Graphical view]
PfamiPF00294. PfkB. 1 hit.
[Graphical view]
PRINTSiPR00990. RIBOKINASE.
SUPFAMiSSF53613. SSF53613. 1 hit.
TIGRFAMsiTIGR02152. D_ribokin_bact. 1 hit.
PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Ribokinase from Escherichia coli K12. Nucleotide sequence and overexpression of the rbsK gene and purification of ribokinase."
    Hope J.N., Bell A.W., Hermodson M.A., Groarke J.M.
    J. Biol. Chem. 261:7663-7668(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-21 AND 297-309, FUNCTION, CATALYTIC ACTIVITY.
    Strain: K12.
  2. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
    Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
    Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Purification, characterization, and crystallization of Escherichia coli ribokinase."
    Sigrell J.A., Cameron A.D., Jones T.A., Mowbray S.L.
    Protein Sci. 6:2474-2476(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
    Strain: K12.
  6. "The effect of inorganic phosphate on the activity of bacterial ribokinase."
    Maj M.C., Gupta R.S.
    J. Protein Chem. 20:139-144(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
  7. Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, ENZYME REGULATION.
  8. "Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8-A resolution: insights into a new family of kinase structures."
    Sigrell J.A., Cameron A.D., Jones T.A., Mowbray S.L.
    Structure 6:183-193(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) IN COMPLEX WITH AMP-PNP AND RIBOSE.
    Strain: K12.
  9. "Induced fit on sugar binding activates ribokinase."
    Sigrell J.A., Cameron A.D., Mowbray S.L.
    J. Mol. Biol. 290:1009-1018(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH ADP; MAGNESIUM AND RIBOSE.
  10. "Activation of ribokinase by monovalent cations."
    Andersson C.E., Mowbray S.L.
    J. Mol. Biol. 315:409-419(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.34 ANGSTROMS) IN COMPLEX WITH ATP ANALOG; CESIUM AND RIBOSE, ENZYME REGULATION.

Entry informationi

Entry nameiRBSK_ECOLI
AccessioniPrimary (citable) accession number: P0A9J6
Secondary accession number(s): P05054, Q2M870
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: July 6, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.