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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

Miscellaneous

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

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)DescriptionActionsGraphical viewLength
Binding sitei149SubstrateUniRule annotation1
Binding sitei193ATPUniRule annotation1
Metal bindingi277PotassiumUniRule annotation1
Metal bindingi279Potassium; via carbonyl oxygenUniRule annotation1
Active sitei283Proton acceptorUniRule annotation1
Binding sitei283SubstrateUniRule annotation1
Metal bindingi313Potassium; via carbonyl oxygenUniRule annotation1
Metal bindingi316Potassium; via carbonyl oxygenUniRule annotation1
Metal bindingi318Potassium; via carbonyl oxygenUniRule annotation1
Metal bindingi322PotassiumUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi248 – 253ATPUniRule annotation6
Nucleotide bindingi282 – 283ATPUniRule annotation2

GO - Molecular functioni

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

GO - Biological processi

  • carbohydrate phosphorylation Source: GO_Central
  • D-ribose catabolic process Source: UniProtKB-UniPathway
  • D-ribose metabolic process Source: SGD

Keywordsi

Molecular functionKinase, Transferase
Biological processCarbohydrate metabolism
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Potassium

Enzyme and pathway databases

BioCyciYEAST:YCR036W-MONOMER.
ReactomeiR-SCE-71336. Pentose phosphate pathway (hexose monophosphate shunt).
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

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000800941 – 333RibokinaseAdd BLAST333

Proteomic databases

MaxQBiP25332.
PRIDEiP25332.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

BioGridi31019. 119 interactors.
DIPiDIP-4990N.
IntActiP25332. 2 interactors.
MINTiMINT-551300.

Structurei

3D structure databases

ProteinModelPortaliP25332.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 12Substrate bindingUniRule annotation3
Regioni38 – 42Substrate bindingUniRule annotation5

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00390000005743.
HOGENOMiHOG000235950.
InParanoidiP25332.
KOiK00852.
OMAiVNQHEVA.
OrthoDBiEOG092C3WGL.

Family and domain databases

CDDicd01174. ribokinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01987. Ribokinase. 1 hit.
InterProiView protein in InterPro
IPR002173. Carboh/pur_kinase_PfkB_CS.
IPR011877. D_ribokin.
IPR011611. PfkB_dom.
IPR002139. Ribo/fructo_kinase.
IPR029056. Ribokinase-like.
PfamiView protein in Pfam
PF00294. PfkB. 1 hit.
PRINTSiPR00990. RIBOKINASE.
SUPFAMiSSF53613. SSF53613. 1 hit.
PROSITEiView protein in PROSITE
PS00584. PFKB_KINASES_2. 1 hit.

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)DescriptionActionsGraphical viewLength
Sequence conflicti178A → T in CAA40228 (PubMed:1964349).Curated1
Sequence conflicti301T → M in CAA40228 (PubMed:1964349).Curated1

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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31019. 119 interactors.
DIPiDIP-4990N.
IntActiP25332. 2 interactors.
MINTiMINT-551300.

Proteomic databases

MaxQBiP25332.
PRIDEiP25332.

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.
OMAiVNQHEVA.
OrthoDBiEOG092C3WGL.

Enzyme and pathway databases

UniPathwayiUPA00916; UER00889.
BioCyciYEAST:YCR036W-MONOMER.
ReactomeiR-SCE-71336. Pentose phosphate pathway (hexose monophosphate shunt).

Miscellaneous databases

PROiPR:P25332.

Family and domain databases

CDDicd01174. ribokinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01987. Ribokinase. 1 hit.
InterProiView protein in InterPro
IPR002173. Carboh/pur_kinase_PfkB_CS.
IPR011877. D_ribokin.
IPR011611. PfkB_dom.
IPR002139. Ribo/fructo_kinase.
IPR029056. Ribokinase-like.
PfamiView protein in Pfam
PF00294. PfkB. 1 hit.
PRINTSiPR00990. RIBOKINASE.
SUPFAMiSSF53613. SSF53613. 1 hit.
PROSITEiView protein in PROSITE
PS00584. PFKB_KINASES_2. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRBSK_YEAST
AccessioniPrimary (citable) accession number: P25332
Secondary accession number(s): D6VR46
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: March 15, 2004
Last modified: June 7, 2017
This is version 140 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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.