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Protein

dTDP-4-dehydrorhamnose reductase

Gene

rfbD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

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

Catalytic activityi

dTDP-beta-L-rhamnose + NADP+ = dTDP-4-dehydro-beta-L-rhamnose + NADPH.1 Publication

Cofactori

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

Kineticsi

  1. KM=0.11 mM for dTDP-6-deoxy-L-mannose (at pH 6.5)1 Publication

    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
    Binding sitei30NADCombined sources1 Publication1
    Binding sitei102NADP; via carbonyl oxygenCombined sources1 Publication1
    Sitei104Could provide a fine-tuning to achieve optimal pKa matching between active site and substrate1 Publication1
    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
    Nucleotide bindingi10 – 12NAD or NADPCombined sources1 Publication3
    Nucleotide bindingi39 – 40NAD or NADPCombined sources1 Publication2
    Nucleotide bindingi63 – 65NAD or NADPCombined sources1 Publication3

    GO - Molecular functioni

    • dTDP-4-dehydrorhamnose reductase activity Source: UniProtKB
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    • dTDP-rhamnose biosynthetic process Source: UniProtKB-UniPathway
    • extracellular polysaccharide biosynthetic process Source: UniProtKB
    • lipopolysaccharide biosynthetic process Source: UniProtKB
    • O antigen biosynthetic process Source: UniProtKB-UniPathway

    Keywordsi

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

    Enzyme and pathway databases

    BioCyciSENT99287:G1FZD-2115-MONOMER
    SABIO-RKiP26392
    UniPathwayiUPA00124
    UPA00281

    Names & Taxonomyi

    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
    Gene namesi
    Name:rfbD
    Synonyms:rmlD
    Ordered Locus Names:STM2096
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    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

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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002079861 – 299dTDP-4-dehydrorhamnose reductaseAdd BLAST299

    Proteomic databases

    PaxDbiP26392
    PRIDEiP26392

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM2096

    Structurei

    Secondary structure

    1299
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 6Combined sources5
    Helixi11 – 19Combined sources9
    Turni20 – 23Combined sources4
    Beta strandi24 – 29Combined sources6
    Beta strandi34 – 36Combined sources3
    Helixi43 – 53Combined sources11
    Beta strandi56 – 60Combined sources5
    Helixi67 – 70Combined sources4
    Helixi74 – 81Combined sources8
    Helixi83 – 92Combined sources10
    Turni93 – 96Combined sources4
    Beta strandi98 – 104Combined sources7
    Helixi105 – 107Combined sources3
    Beta strandi112 – 114Combined sources3
    Helixi127 – 142Combined sources16
    Beta strandi144 – 151Combined sources8
    Beta strandi153 – 155Combined sources3
    Beta strandi157 – 159Combined sources3
    Helixi162 – 172Combined sources11
    Beta strandi174 – 179Combined sources6
    Helixi189 – 205Combined sources17
    Helixi207 – 209Combined sources3
    Beta strandi211 – 214Combined sources4
    Helixi223 – 237Combined sources15
    Beta strandi245 – 249Combined sources5
    Helixi251 – 253Combined sources3
    Beta strandi262 – 264Combined sources3
    Helixi269 – 275Combined sources7
    Helixi282 – 294Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    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...

    Miscellaneous databases

    EvolutionaryTraceiP26392

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni104 – 105Substrate bindingCombined sources1 Publication2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DBZ Bacteria
    COG1091 LUCA
    HOGENOMiHOG000227712
    KOiK00067
    OMAiYHYSNEG
    PhylomeDBiP26392

    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

    Sequencei

    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
    Checksum:iABAA0476AF5ECDE7
    GO

    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

    Genome annotation databases

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

    Similar proteinsi

    Entry informationi

    Entry nameiRMLD_SALTY
    AccessioniPrimary (citable) accession number: P26392
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: August 1, 1992
    Last modified: June 20, 2018
    This is version 127 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

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