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Protein

dTDP-4-dehydrorhamnose reductase

Gene

rfbD

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

Involved in the biosynthesis of the dTDP-L-rhamnose which is an important component of lipopolysaccharide (LPS). Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.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 provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per monomer. Mg2+ is important for dimerization.1 Publication

<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

  1. KM=0.11 mM for dTDP-6-deoxy-L-mannose (at pH 6.5)1 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.By similarity
    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.By similarity
    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 sitei30NADCombined sources1 Publication1
    Binding sitei102NADP; via carbonyl oxygenCombined sources1 Publication1
    <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>Sitei104Could provide a fine-tuning to achieve optimal pKa matching between active site and substrate1 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 sitei128Proton donor/acceptorCombined sources1 Publication1
    Binding sitei132NAD or NADPCombined sources1 Publication1
    Binding sitei153Substrate; via amide nitrogenCombined sources1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi10 – 12NAD or NADPCombined sources1 Publication3
    Nucleotide bindingi39 – 40NAD or NADPCombined sources1 Publication2
    Nucleotide bindingi63 – 65NAD or NADPCombined sources1 Publication3

    <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 reductase activity Source: UniProtKB
    • metal ion binding Source: UniProtKB-KW

    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 functionOxidoreductase
    Biological processCarbohydrate metabolism, Lipopolysaccharide biosynthesis
    LigandMagnesium, Metal-binding, NAD, NADP

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    SENT99287:STM2096-MONOMER

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    P26392

    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 reductaseCurated (EC:1.1.1.1331 Publication)
    Alternative name(s):
    dTDP-4-keto-L-rhamnose reductaseCurated
    dTDP-6-deoxy-L-lyxo-4-hexulose reductase1 Publication
    dTDP-6-deoxy-L-mannose dehydrogenaseCurated
    dTDP-L-rhamnose synthaseCurated
    <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:rfbD
    Synonyms:rmlD
    Ordered Locus Names:STM2096
    <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 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

    • cytosol Source: GO_Central

    <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>Mutagenesisi67V → A: Significantly reduces enzyme activity. 1 Publication1
    Mutagenesisi68D → A: Slightly reduces enzyme activity. 1 Publication1
    Mutagenesisi104T → A: Loss of activity. 1 Publication1
    Mutagenesisi128Y → F: Loss of activity. 1 Publication1
    Mutagenesisi153W → A: Loss of activity. 1 Publication1

    Chemistry databases

    Drug and drug target database

    More...
    DrugBanki
    DB03723 2'-Deoxy-Thymidine-Beta-L-Rhamnose

    <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_00002079861 – 299dTDP-4-dehydrorhamnose reductaseAdd BLAST299

    Proteomic databases

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

    More...
    PaxDbi
    P26392

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P26392

    <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.STM2096

    <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

    1299
    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
    P26392

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

    More...
    SMRi
    P26392

    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
    P26392

    <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>Regioni104 – 105Substrate bindingCombined sources1 Publication2

    <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
    ENOG4105DBZ Bacteria
    COG1091 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000227712

    KEGG Orthology (KO)

    More...
    KOi
    K00067

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    YHYSNEG

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P26392

    Family and domain databases

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR005913 dTDP_dehydrorham_reduct
    IPR036291 NAD(P)-bd_dom_sf
    IPR029903 RmlD-like-bd

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR10491 PTHR10491, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF04321 RmlD_sub_bind, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51735 SSF51735, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01214 rmlD, 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.

    P26392-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MNILLFGKTG QVGWELQRSL APVGNLIALD VHSKEFCGDF SNPKGVAETV
    60 70 80 90 100
    RKLRPDVIVN AAAHTAVDKA ESEPELAQLL NATSVEAIAK AANETGAWVV
    110 120 130 140 150
    HYSTDYVFPG TGDIPWQETD ATSPLNVYGK TKLAGEKALQ DNCPKHLIFR
    160 170 180 190 200
    TSWVYAGKGN NFAKTMLRLA KERQTLSVIN DQYGAPTGAE LLADCTAHAI
    210 220 230 240 250
    RVALNKPEVA GLYHLVAGGT TTWHDYAALV FDEARKAGIT LALTELNAVP
    260 270 280 290
    TSAYPTPASR PGNSRLNTEK FQRNFDLILP QWELGVKRML TEMFTTTTI
    Length:299
    Mass (Da):32,554
    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:iABAA0476AF5ECDE7
    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: CAA40116.1
    AE006468 Genomic DNA Translation: AAL21000.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    S15300

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_461041.1, NC_003197.2
    WP_001023662.1, NC_003197.2

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAL21000; AAL21000; STM2096

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    1253617

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    stm:STM2096

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|99287.12.peg.2218

    <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: CAA40116.1
    AE006468 Genomic DNA Translation: AAL21000.1
    PIRiS15300
    RefSeqiNP_461041.1, NC_003197.2
    WP_001023662.1, 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
    1KBZX-ray2.20A1-299[»]
    1KC1X-ray2.60A1-299[»]
    1KC3X-ray2.70A1-299[»]
    1N2SX-ray2.00A1-299[»]
    ProteinModelPortaliP26392
    SMRiP26392
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM2096

    Chemistry databases

    DrugBankiDB03723 2'-Deoxy-Thymidine-Beta-L-Rhamnose

    Proteomic databases

    PaxDbiP26392
    PRIDEiP26392

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL21000; AAL21000; STM2096
    GeneIDi1253617
    KEGGistm:STM2096
    PATRICifig|99287.12.peg.2218

    Phylogenomic databases

    eggNOGiENOG4105DBZ Bacteria
    COG1091 LUCA
    HOGENOMiHOG000227712
    KOiK00067
    OMAiYHYSNEG
    PhylomeDBiP26392

    Enzyme and pathway databases

    UniPathwayi
    UPA00124

    UPA00281

    BioCyciSENT99287:STM2096-MONOMER
    SABIO-RKiP26392

    Miscellaneous databases

    EvolutionaryTraceiP26392

    Family and domain databases

    InterProiView protein in InterPro
    IPR005913 dTDP_dehydrorham_reduct
    IPR036291 NAD(P)-bd_dom_sf
    IPR029903 RmlD-like-bd
    PANTHERiPTHR10491 PTHR10491, 1 hit
    PfamiView protein in Pfam
    PF04321 RmlD_sub_bind, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit
    TIGRFAMsiTIGR01214 rmlD, 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 nameiRMLD_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: P26392
    <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 129 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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