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Protein

Ribokinase

Gene

rbsK

Organism
Shigella boydii serotype 4 (strain Sb227)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 annotation

Catalytic activityi

ATP + D-ribose = ADP + D-ribose 5-phosphate.UniRule annotation

Cofactori

Mg2+UniRule annotationNote: 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.UniRule annotation

Enzyme regulationi

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.UniRule annotation

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 annotation
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 annotation
Binding sitei187 – 1871ATPUniRule annotation
Metal bindingi249 – 2491PotassiumUniRule annotation
Metal bindingi251 – 2511Potassium; via carbonyl oxygenUniRule annotation
Active sitei255 – 2551Proton acceptorUniRule annotation
Binding sitei255 – 2551SubstrateUniRule annotation
Binding sitei279 – 2791ATPUniRule annotation
Metal bindingi285 – 2851Potassium; via carbonyl oxygenUniRule annotation
Metal bindingi288 – 2881Potassium; via carbonyl oxygenUniRule annotation
Metal bindingi290 – 2901Potassium; via carbonyl oxygenUniRule annotation
Metal bindingi294 – 2941PotassiumUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi223 – 2286ATPUniRule annotation
Nucleotide bindingi254 – 2552ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

KinaseUniRule annotationSAAS annotationImported, Transferase

Keywords - Biological processi

Carbohydrate metabolismUniRule annotation

Keywords - Ligandi

ATP-bindingUniRule annotation, MagnesiumUniRule annotation, Metal-bindingUniRule annotation, Nucleotide-binding, PotassiumUniRule annotation

Enzyme and pathway databases

BioCyciSBOY300268:GJFL-3763-MONOMER.
UniPathwayiUPA00916; UER00889.

Names & Taxonomyi

Protein namesi
Recommended name:
RibokinaseUniRule annotation (EC:2.7.1.15UniRule annotation)
Short name:
RKUniRule annotation
Gene namesi
Name:rbsKUniRule annotationImported
Ordered Locus Names:SBO_3766Imported
OrganismiShigella boydii serotype 4 (strain Sb227)Imported
Taxonomic identifieri300268 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
Proteomesi
  • UP000007067 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

Keywords - Cellular componenti

CytoplasmUniRule annotation

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliQ31UM3.
SMRiQ31UM3. Positions 2-308.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 297292PfkBInterPro annotationAdd
BLAST

Region

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

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000235950.
KOiK00852.
OMAiNADHVIS.
OrthoDBiEOG64JFMD.

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.

Q31UM3-1 [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:December 6, 2005 - v1
Checksum:i753729B41E64060E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000036 Genomic DNA. Translation: ABB68235.1.
RefSeqiWP_001300603.1. NC_007613.1.

Genome annotation databases

EnsemblBacteriaiABB68235; ABB68235; SBO_3766.
KEGGisbo:SBO_3766.
PATRICi18687319. VBIShiBoy33460_4536.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000036 Genomic DNA. Translation: ABB68235.1.
RefSeqiWP_001300603.1. NC_007613.1.

3D structure databases

ProteinModelPortaliQ31UM3.
SMRiQ31UM3. Positions 2-308.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB68235; ABB68235; SBO_3766.
KEGGisbo:SBO_3766.
PATRICi18687319. VBIShiBoy33460_4536.

Phylogenomic databases

HOGENOMiHOG000235950.
KOiK00852.
OMAiNADHVIS.
OrthoDBiEOG64JFMD.

Enzyme and pathway databases

UniPathwayiUPA00916; UER00889.
BioCyciSBOY300268:GJFL-3763-MONOMER.

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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Sb227Imported.

Entry informationi

Entry nameiQ31UM3_SHIBS
AccessioniPrimary (citable) accession number: Q31UM3
Entry historyi
Integrated into UniProtKB/TrEMBL: December 6, 2005
Last sequence update: December 6, 2005
Last modified: July 6, 2016
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.