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Protein

dTDP-4-dehydrorhamnose 3,5-epimerase

Gene

rfbC

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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 epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.1 Publication

<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 ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

Kcat is 39 sec(-1) with dTDP-6-deoxy-D-xylo-4-hexulose as substrate.1 Publication
  1. KM=0.71 mM for dTDP-6-deoxy-D-xylo-4-hexulose1 Publication

    <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: dTDP-L-rhamnose biosynthesis

    This protein is involved in the pathway dTDP-L-rhamnose biosynthesis, which is part of Carbohydrate biosynthesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway dTDP-L-rhamnose biosynthesis and in Carbohydrate biosynthesis.

    Pathwayi: LPS O-antigen biosynthesis

    This protein is involved in the pathway LPS O-antigen biosynthesis, which is part of Bacterial outer membrane biogenesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway LPS O-antigen biosynthesis and in Bacterial outer membrane biogenesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ 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 sitei24SubstrateBy similarity1
    Binding sitei29SubstrateCombined sources1 Publication1
    Binding sitei60SubstrateCombined sources1 Publication1
    <p>This subsection of the ‘Function’ 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 sitei63Proton acceptorCombined sources2 Publications1
    Binding sitei73SubstrateCombined sources1 Publication1
    Binding sitei120SubstrateCombined sources1 Publication1
    Active sitei133Proton donorCombined sources2 Publications1
    <p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei139Participates in a stacking interaction with the thymidine ring of dTDP-4-oxo-6-deoxyglucoseBy similarity1
    Binding sitei144SubstrateBy similarity1
    Binding sitei169SubstrateCombined sources1 Publication1

    <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

    • dTDP-4-dehydrorhamnose 3,5-epimerase activity Source: UniProtKB

    GO - Biological processi

    <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, Lipopolysaccharide biosynthesis

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    SENT99287:STM2094-MONOMER

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    P26394

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

    More...
    UniPathwayi
    UPA00124

    UPA00281

    <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:
    dTDP-4-dehydrorhamnose 3,5-epimerase1 Publication (EC:5.1.3.131 Publication)
    Alternative name(s):
    Thymidine diphospho-4-keto-rhamnose 3,5-epimerase1 Publication
    dTDP-4-keto-6-deoxyglucose 3,5-epimerase1 Publication
    dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase1 Publication
    dTDP-L-rhamnose synthase1 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:rfbC1 Publication
    Synonyms:rmlC
    Ordered Locus Names:STM2094
    <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>OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    <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 identifieri99287 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    <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
    • UP000001014 <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

    <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>Mutagenesisi63H → A: Loss of epimerase activity. 1 Publication1
    Mutagenesisi73K → A: Reduces the epimerase activity by over 100-fold. 1 Publication1
    Mutagenesisi133Y → F: Reduces the epimerase activity by over 1000-fold. 1 Publication1

    Chemistry databases

    Drug and drug target database

    More...
    DrugBanki
    DB02549 3'-O-Acetylthymidine-5'-Diphosphate

    <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_00002079791 – 183dTDP-4-dehydrorhamnose 3,5-epimeraseAdd BLAST183

    Proteomic databases

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

    More...
    PaxDbi
    P26394

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P26394

    <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

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    99287.STM2094

    <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

    Secondary structure

    1183
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    P26394

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

    More...
    SMRi
    P26394

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    P26394

    <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>Regioni48 – 50Substrate bindingCombined sources1 Publication3

    <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

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4108URP Bacteria
    COG1898 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000227724

    KEGG Orthology (KO)

    More...
    KOi
    K01790

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    RGVFLEW

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P26394

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    2.60.120.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR000888 dTDP_sugar_isom
    IPR014710 RmlC-like_jellyroll
    IPR011051 RmlC_Cupin_sf

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR21047 PTHR21047, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00908 dTDP_sugar_isom, 1 hit

    ProDom; a protein domain database

    More...
    ProDomi
    View protein in ProDom or Entries sharing at least one domain
    PD001462 dTDP_sugar_isom, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51182 SSF51182, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01221 rmlC, 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>.<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.

    P26394-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MMIVIKTAIP DVLILEPKVF GDERGFFFES YNQQTFEELI GRKVTFVQDN
    60 70 80 90 100
    HSKSKKNVLR GLHFQRGENA QGKLVRCAVG EVFDVAVDIR KESPTFGQWV
    110 120 130 140 150
    GVNLSAENKR QLWIPEGFAH GFVTLSEYAE FLYKATNYYS PSSEGSILWN
    160 170 180
    DEAIGIEWPF SQLPELSAKD AAAPLLDQAL LTE
    Length:183
    Mass (Da):20,663
    Last modified:August 1, 1992 - v1
    <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:i0176B52C38038C77
    GO

    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
    X56793 Genomic DNA Translation: CAA40118.1
    AE006468 Genomic DNA Translation: AAL20998.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    S15302

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_461039.1, NC_003197.2
    WP_000973708.1, NC_003197.2

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAL20998; AAL20998; STM2094

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    1253615

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    stm:STM2094

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|99287.12.peg.2216

    <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
    X56793 Genomic DNA Translation: CAA40118.1
    AE006468 Genomic DNA Translation: AAL20998.1
    PIRiS15302
    RefSeqiNP_461039.1, NC_003197.2
    WP_000973708.1, NC_003197.2

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1DZRX-ray2.17A/B1-183[»]
    1DZTX-ray2.20A/B1-183[»]
    ProteinModelPortaliP26394
    SMRiP26394
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM2094

    Chemistry databases

    DrugBankiDB02549 3'-O-Acetylthymidine-5'-Diphosphate

    Proteomic databases

    PaxDbiP26394
    PRIDEiP26394

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL20998; AAL20998; STM2094
    GeneIDi1253615
    KEGGistm:STM2094
    PATRICifig|99287.12.peg.2216

    Phylogenomic databases

    eggNOGiENOG4108URP Bacteria
    COG1898 LUCA
    HOGENOMiHOG000227724
    KOiK01790
    OMAiRGVFLEW
    PhylomeDBiP26394

    Enzyme and pathway databases

    UniPathwayi
    UPA00124

    UPA00281

    BioCyciSENT99287:STM2094-MONOMER
    SABIO-RKiP26394

    Miscellaneous databases

    EvolutionaryTraceiP26394

    Family and domain databases

    Gene3Di2.60.120.10, 1 hit
    InterProiView protein in InterPro
    IPR000888 dTDP_sugar_isom
    IPR014710 RmlC-like_jellyroll
    IPR011051 RmlC_Cupin_sf
    PANTHERiPTHR21047 PTHR21047, 1 hit
    PfamiView protein in Pfam
    PF00908 dTDP_sugar_isom, 1 hit
    ProDomiView protein in ProDom or Entries sharing at least one domain
    PD001462 dTDP_sugar_isom, 1 hit
    SUPFAMiSSF51182 SSF51182, 1 hit
    TIGRFAMsiTIGR01221 rmlC, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    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 nameiRMLC_SALTY
    <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: P26394
    <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 1, 1992
    Last sequence update: August 1, 1992
    Last modified: December 5, 2018
    This is version 126 of the entry and version 1 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
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