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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)DescriptionActionsGraphical viewLength
Active sitei20Proton donorCurated1
Binding sitei28SubstrateBy similarity1
Binding sitei106SubstrateBy similarity1

GO - Molecular functioni

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

GO - Biological processi

  • D-ribose catabolic process Source: EcoCyc

Keywordsi

Molecular functionIsomerase
Biological processCarbohydrate metabolism

Enzyme and pathway databases

BioCyciEcoCyc:EG10817-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10817. rbsD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi20H → A: Loss of pyranase activity. 1 Publication1
Mutagenesisi106H → A: Retains one-third of the original activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000971921 – 139D-ribose pyranaseAdd BLAST139

Proteomic databases

EPDiP04982.
PaxDbiP04982.
PRIDEiP04982.

Interactioni

Subunit structurei

Homodecamer.2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4261236. 7 interactors.
STRINGi316385.ECDH10B_3936.

Structurei

3D structure databases

ProteinModelPortaliP04982.
SMRiP04982.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni128 – 130Substrate bindingBy similarity3

Sequence similaritiesi

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

Phylogenomic databases

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

Family and domain databases

Gene3Di3.40.1650.10. 1 hit.
HAMAPiMF_01661. D_rib_pyranase. 1 hit.
InterProiView protein in InterPro
IPR023064. D-ribose_pyranase.
IPR023750. RbsD-like.
IPR007721. RbsD_FucU.
PfamiView protein in Pfam
PF05025. RbsD_FucU. 1 hit.
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 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.
PATRICifig|1411691.4.peg.2952.

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.

Entry informationi

Entry nameiRBSD_ECOLI
AccessioniPrimary (citable) accession number: P04982
Secondary accession number(s): Q2M866
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: July 19, 2004
Last modified: July 5, 2017
This is version 131 of the entry and version 3 of the sequence. See 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