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Entry version 145 (18 Sep 2019)
Sequence version 3 (19 Jul 2004)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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), D-ribose pyranase (rbsD), D-ribose pyranase (rbsD), D-ribose pyranase (rbsD)
  2. Ribokinase (rbsK), Ribokinase (rbsK), Ribokinase (rbsK), Ribokinase (rbsK), Ribokinase (rbsK), 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
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei20Proton donorCurated1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei28SubstrateBy similarity1
Binding sitei106SubstrateBy similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

  • D-ribose catabolic process Source: EcoCyc

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionIsomerase
Biological processCarbohydrate metabolism

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG10817-MONOMER
ECOL316407:JW5857-MONOMER
MetaCyc:EG10817-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
5.4.99.62 2026

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00916;UER00888

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
D-ribose pyranase (EC:5.4.99.621 Publication)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rbsD
Ordered Locus Names:b3748, JW5857
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

Escherichia coli strain K12 genome database

More...
EcoGenei
EG10817 rbsD

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi20H → A: Loss of pyranase activity. 1 Publication1
Mutagenesisi106H → A: Retains one-third of the original activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000971921 – 139D-ribose pyranaseAdd BLAST139

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
P04982

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P04982

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P04982

PRoteomics IDEntifications database

More...
PRIDEi
P04982

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodecamer.

2 Publications

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4261236, 14 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3748

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P04982

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni128 – 130Substrate bindingBy similarity3

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105MRB Bacteria
COG1869 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000219040

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P04982

KEGG Orthology (KO)

More...
KOi
K06726

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P04982

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.1650.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01661 D_rib_pyranase, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR023064 D-ribose_pyranase
IPR023750 RbsD-like_sf
IPR007721 RbsD_FucU

The PANTHER Classification System

More...
PANTHERi
PTHR37831 PTHR37831, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF05025 RbsD_FucU, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF102546 SSF102546, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iD19A9D98CB79F611
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

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

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

More...
PIRi
E65178

NCBI Reference Sequences

More...
RefSeqi
NP_418204.2, NC_000913.3
WP_001301979.1, NZ_SSZK01000036.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76771; AAC76771; b3748
BAE77540; BAE77540; BAE77540

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
948267

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW5857
eco:b3748

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.2952

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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_SSZK01000036.1

3D structure databases

SMRiP04982
ModBaseiSearch...

Protein-protein interaction databases

BioGridi4261236, 14 interactors
STRINGi511145.b3748

Proteomic databases

EPDiP04982
jPOSTiP04982
PaxDbiP04982
PRIDEiP04982

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76771; AAC76771; b3748
BAE77540; BAE77540; BAE77540
GeneIDi948267
KEGGiecj:JW5857
eco:b3748
PATRICifig|1411691.4.peg.2952

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB0810
EcoGeneiEG10817 rbsD

Phylogenomic databases

eggNOGiENOG4105MRB Bacteria
COG1869 LUCA
HOGENOMiHOG000219040
InParanoidiP04982
KOiK06726
PhylomeDBiP04982

Enzyme and pathway databases

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

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P04982

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_sf
IPR007721 RbsD_FucU
PANTHERiPTHR37831 PTHR37831, 1 hit
PfamiView protein in Pfam
PF05025 RbsD_FucU, 1 hit
SUPFAMiSSF102546 SSF102546, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRBSD_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P04982
Secondary accession number(s): Q2M866
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: July 19, 2004
Last modified: September 18, 2019
This is version 145 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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