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Protein

Ribokinase

Gene

RBK1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 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 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. no protein annotated in this organism
  2. Ribokinase (RBK1)
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 sitei149 – 1491SubstrateUniRule annotation
Binding sitei193 – 1931ATPUniRule annotation
Metal bindingi277 – 2771PotassiumUniRule annotation
Metal bindingi279 – 2791Potassium; via carbonyl oxygenUniRule annotation
Active sitei283 – 2831Proton acceptorUniRule annotation
Binding sitei283 – 2831SubstrateUniRule annotation
Metal bindingi313 – 3131Potassium; via carbonyl oxygenUniRule annotation
Metal bindingi316 – 3161Potassium; via carbonyl oxygenUniRule annotation
Metal bindingi318 – 3181Potassium; via carbonyl oxygenUniRule annotation
Metal bindingi322 – 3221PotassiumUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi248 – 2536ATPUniRule annotation
Nucleotide bindingi282 – 2832ATPUniRule annotation

GO - Molecular functioni

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

GO - Biological processi

  • D-ribose catabolic process Source: UniProtKB-HAMAP
  • D-ribose metabolic process Source: SGD
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

BioCyciYEAST:YCR036W-MONOMER.
UniPathwayiUPA00916; UER00889.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribokinase1 PublicationUniRule annotation (EC:2.7.1.15UniRule annotationBy similarity)
Short name:
RKUniRule annotation
Gene namesi
Name:RBK11 PublicationUniRule annotation
Ordered Locus Names:YCR036WImported
ORF Names:YCR36W, YCR523
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:YCR036W.
SGDiS000000632. RBK1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 333333RibokinasePRO_0000080094Add
BLAST

Proteomic databases

MaxQBiP25332.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

BioGridi31019. 82 interactions.
DIPiDIP-4990N.
IntActiP25332. 2 interactions.
MINTiMINT-551300.

Structurei

3D structure databases

ProteinModelPortaliP25332.
SMRiP25332. Positions 2-329.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 123Substrate bindingUniRule annotation
Regioni38 – 425Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00390000005743.
HOGENOMiHOG000235950.
InParanoidiP25332.
KOiK00852.
OMAiTAVLIMN.
OrthoDBiEOG092C3WGL.

Family and domain databases

Gene3Di3.40.1190.20. 2 hits.
HAMAPiMF_01987. Ribokinase. 1 hit.
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.
PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25332-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGITVIGSLN YDLDTFTDRL PNAGETFRAN HFETHAGGKG LNQAAAIGKL
60 70 80 90 100
KNPSSRYSVR MIGNVGNDTF GKQLKDTLSD CGVDITHVGT YEGINTGTAT
110 120 130 140 150
ILIEEKAGGQ NRILIVEGAN SKTIYDPKQL CEIFPEGKEE EEYVVFQHEI
160 170 180 190 200
PDPLSIIKWI HANRPNFQIV YNPSPFKAMP KKDWELVDLL VVNEIEGLQI
210 220 230 240 250
VESVFDNELV EEIREKIKDD FLGEYRKICE LLYEKLMNRK KRGIVVMTLG
260 270 280 290 300
SRGVLFCSHE SPEVQFLPAI QNVSVVDTTG AGDTFLGGLV TQLYQGETLS
310 320 330
TAIKFSTLAS SLTIQRKGAA ESMPLYKDVQ KDA
Length:333
Mass (Da):36,924
Last modified:March 15, 2004 - v2
Checksum:i226B44DA7E458B95
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti178 – 1781A → T in CAA40228 (PubMed:1964349).Curated
Sequence conflicti301 – 3011T → M in CAA40228 (PubMed:1964349).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56909 Genomic DNA. Translation: CAA40228.1.
X59720 Genomic DNA. Translation: CAA42303.2.
BK006937 Genomic DNA. Translation: DAA07515.1.
PIRiS12918. KIBYRB.
RefSeqiNP_009965.2. NM_001178750.1.

Genome annotation databases

EnsemblFungiiCAA42303; CAA42303; CAA42303.
YCR036W; YCR036W; YCR036W.
GeneIDi850402.
KEGGisce:YCR036W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56909 Genomic DNA. Translation: CAA40228.1.
X59720 Genomic DNA. Translation: CAA42303.2.
BK006937 Genomic DNA. Translation: DAA07515.1.
PIRiS12918. KIBYRB.
RefSeqiNP_009965.2. NM_001178750.1.

3D structure databases

ProteinModelPortaliP25332.
SMRiP25332. Positions 2-329.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31019. 82 interactions.
DIPiDIP-4990N.
IntActiP25332. 2 interactions.
MINTiMINT-551300.

Proteomic databases

MaxQBiP25332.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAA42303; CAA42303; CAA42303.
YCR036W; YCR036W; YCR036W.
GeneIDi850402.
KEGGisce:YCR036W.

Organism-specific databases

EuPathDBiFungiDB:YCR036W.
SGDiS000000632. RBK1.

Phylogenomic databases

GeneTreeiENSGT00390000005743.
HOGENOMiHOG000235950.
InParanoidiP25332.
KOiK00852.
OMAiTAVLIMN.
OrthoDBiEOG092C3WGL.

Enzyme and pathway databases

UniPathwayiUPA00916; UER00889.
BioCyciYEAST:YCR036W-MONOMER.

Miscellaneous databases

PROiP25332.

Family and domain databases

Gene3Di3.40.1190.20. 2 hits.
HAMAPiMF_01987. Ribokinase. 1 hit.
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.
PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRBSK_YEAST
AccessioniPrimary (citable) accession number: P25332
Secondary accession number(s): D6VR46
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: March 15, 2004
Last modified: September 7, 2016
This is version 133 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1780 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome III
    Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

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.