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Protein

D-ribose pyranase

Gene

rbsD

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

Functioni

Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. It also catalyzes the conversion between beta-allofuranose and beta-allopyranose.1 Publication

Catalytic activityi

Beta-D-ribopyranose = beta-D-ribofuranose.1 Publication
Beta-D-allopyranose = beta-D-allofuranose.1 Publication

Pathwayi: D-ribose degradation

This protein is involved in step 1 of the subpathway that synthesizes D-ribose 5-phosphate from beta-D-ribopyranose.
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
Active sitei20 – 201Proton donorCurated
Binding sitei28 – 281SubstrateBy similarity
Binding sitei106 – 1061SubstrateBy similarity

GO - Molecular functioni

  • identical protein binding Source: EcoCyc
  • intramolecular lyase activity Source: UniProtKB-HAMAP
  • intramolecular transferase activity Source: EcoCyc
  • monosaccharide binding Source: InterPro

GO - Biological processi

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

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Carbohydrate metabolism

Enzyme and pathway databases

BioCyciEcoCyc:EG10817-MONOMER.
ECOL316407:JW5857-MONOMER.
MetaCyc:EG10817-MONOMER.
BRENDAi5.4.99.62. 2026.
UniPathwayiUPA00916; UER00888.

Names & Taxonomyi

Protein namesi
Recommended name:
D-ribose pyranase (EC:5.4.99.621 Publication)
Gene namesi
Name:rbsD
Ordered Locus Names:b3748, JW5857
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10817. rbsD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi20 – 201H → A: Loss of pyranase activity. 1 Publication
Mutagenesisi106 – 1061H → A: Retains one-third of the original activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 139139D-ribose pyranasePRO_0000097192Add
BLAST

Proteomic databases

EPDiP04982.
PaxDbiP04982.

Interactioni

Subunit structurei

Homodecamer.2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4261236. 7 interactions.
STRINGi511145.b3748.

Structurei

3D structure databases

ProteinModelPortaliP04982.
SMRiP04982. Positions 1-139.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni128 – 1303Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the RbsD / FucU family. RbsD subfamily.Curated

Phylogenomic databases

eggNOGiENOG4105MRB. Bacteria.
COG1869. LUCA.
HOGENOMiHOG000219040.
InParanoidiP04982.
KOiK06726.
OMAiIIRTGEC.
OrthoDBiEOG68SW4G.
PhylomeDBiP04982.

Family and domain databases

Gene3Di3.40.1650.10. 1 hit.
HAMAPiMF_01661. D_rib_pyranase.
InterProiIPR023064. D-ribose_pyranase.
IPR023750. RbsD-like.
IPR007721. RbsD_FucU.
[Graphical view]
PfamiPF05025. RbsD_FucU. 1 hit.
[Graphical view]
SUPFAMiSSF102546. SSF102546. 1 hit.

Sequencei

Sequence statusi: Complete.

P04982-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKGTVLNSD ISSVISRLGH TDTLVVCDAG LPIPKSTTRI DMALTQGVPS
60 70 80 90 100
FMQVLGVVTN EMQVEAAIIA EEIKHHNPQL HETLLTHLEQ LQKHQGNTIE
110 120 130
IRYTTHEQFK QQTAESQAVI RSGECSPYAN IILCAGVTF
Length:139
Mass (Da):15,292
Last modified:July 19, 2004 - v3
Checksum:iD19A9D98CB79F611
GO

Sequence cautioni

The sequence AAA62101.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13169 Genomic DNA. Translation: AAA51472.1.
L10328 Genomic DNA. Translation: AAA62101.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76771.2.
AP009048 Genomic DNA. Translation: BAE77540.1.
X68551 Genomic DNA. Translation: CAA48556.1.
PIRiE65178.
RefSeqiNP_418204.2. NC_000913.3.
WP_001301979.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76771; AAC76771; b3748.
BAE77540; BAE77540; BAE77540.
GeneIDi948267.
KEGGiecj:JW5857.
eco:b3748.
PATRICi32122995. VBIEscCol129921_3873.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13169 Genomic DNA. Translation: AAA51472.1.
L10328 Genomic DNA. Translation: AAA62101.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76771.2.
AP009048 Genomic DNA. Translation: BAE77540.1.
X68551 Genomic DNA. Translation: CAA48556.1.
PIRiE65178.
RefSeqiNP_418204.2. NC_000913.3.
WP_001301979.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP04982.
SMRiP04982. Positions 1-139.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261236. 7 interactions.
STRINGi511145.b3748.

Proteomic databases

EPDiP04982.
PaxDbiP04982.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76771; AAC76771; b3748.
BAE77540; BAE77540; BAE77540.
GeneIDi948267.
KEGGiecj:JW5857.
eco:b3748.
PATRICi32122995. VBIEscCol129921_3873.

Organism-specific databases

EchoBASEiEB0810.
EcoGeneiEG10817. rbsD.

Phylogenomic databases

eggNOGiENOG4105MRB. Bacteria.
COG1869. LUCA.
HOGENOMiHOG000219040.
InParanoidiP04982.
KOiK06726.
OMAiIIRTGEC.
OrthoDBiEOG68SW4G.
PhylomeDBiP04982.

Enzyme and pathway databases

UniPathwayiUPA00916; UER00888.
BioCyciEcoCyc:EG10817-MONOMER.
ECOL316407:JW5857-MONOMER.
MetaCyc:EG10817-MONOMER.
BRENDAi5.4.99.62. 2026.

Miscellaneous databases

PROiP04982.

Family and domain databases

Gene3Di3.40.1650.10. 1 hit.
HAMAPiMF_01661. D_rib_pyranase.
InterProiIPR023064. D-ribose_pyranase.
IPR023750. RbsD-like.
IPR007721. RbsD_FucU.
[Graphical view]
PfamiPF05025. RbsD_FucU. 1 hit.
[Graphical view]
SUPFAMiSSF102546. SSF102546. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12."
    Bell A.W., Buckel S.D., Groarke J.M., Hope J.N., Kingsley D.H., Hermodson M.A.
    J. Biol. Chem. 261:7652-7658(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    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. "A role of RnlA in the RNase LS activity from Escherichia coli."
    Otsuka Y., Koga M., Iwamoto A., Yonesaki T.
    Genes Genet. Syst. 82:291-299(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-8.
    Strain: K12.
  6. "Nucleotide sequence and 3'-end deletion studies indicate that the K(+)-uptake protein kup from Escherichia coli is composed of a hydrophobic core linked to a large and partially essential hydrophilic C-terminus."
    Schleyer M., Bakker E.P.
    J. Bacteriol. 175:6925-6931(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-41.
    Strain: K12.
  7. "Crystallization and preliminary X-ray crystallographic analysis of Escherichia coli RbsD, a component of the ribose-transport system with unknown biochemical function."
    Kim M.-S., Oh H., Park C., Oh B.-H.
    Acta Crystallogr. D 57:728-730(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION.
  8. "Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture."
    Kim M.-S., Shin J., Lee W., Lee H.-S., Oh B.-H.
    J. Biol. Chem. 278:28173-28180(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  9. "NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration."
    Ryu K.-S., Kim C., Kim I., Yoo S., Choi B.-S., Park C.
    J. Biol. Chem. 279:25544-25548(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF HIS-20 AND HIS-106, REACTION MECHANISM.
  10. "Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein."
    Feng Y., Jiao W., Fu X., Chang Z.
    Protein Sci. 15:1441-1448(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.

Entry informationi

Entry nameiRBSD_ECOLI
AccessioniPrimary (citable) accession number: P04982
Secondary accession number(s): Q2M866
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: July 19, 2004
Last modified: March 16, 2016
This is version 124 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally thought (PubMed:3011793) to be a high affinity ribose transport protein, but further analysis (PubMed:15060078) shows that it is a D-ribose pyranase.2 Publications

Keywords - Technical termi

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. 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.