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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-Experimental evidence at protein leveli

Functioni

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.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.
    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.
    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 sitei12NAD; via amide nitrogen1
    Binding sitei102NADP; via carbonyl oxygen1
    Binding sitei153Substrate; via amide nitrogen1
    Binding sitei154NAD; via amide nitrogen1
    Binding sitei223Substrate1
    Binding sitei260Substrate1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi7 – 11NAD5
    Nucleotide bindingi11 – 12NADP2
    Nucleotide bindingi30 – 31NAD2
    Nucleotide bindingi39 – 40NAD/NADP2
    Nucleotide bindingi62 – 65NAD4
    Nucleotide bindingi63 – 65NADP3
    Nucleotide bindingi128 – 132NAD/NADP5

    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
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Lipopolysaccharide biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding, NADP

    Enzyme and pathway databases

    SABIO-RKP26392.
    UniPathwayiUPA00124.
    UPA00281.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dTDP-4-dehydrorhamnose reductase (EC:1.1.1.133)
    Alternative name(s):
    dTDP-4-keto-L-rhamnose reductase
    dTDP-6-deoxy-L-lyxo-4-hexulose reductase
    dTDP-6-deoxy-L-mannose dehydrogenase
    dTDP-L-rhamnose synthase
    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

    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 binding2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DBZ. Bacteria.
    COG1091. LUCA.
    HOGENOMiHOG000227712.
    KOiK00067.
    OMAiGYASRYE.
    PhylomeDBiP26392.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR005913. dTDP_dehydrorham_reduct.
    IPR016040. NAD(P)-bd_dom.
    IPR029903. RmlD-like-bd.
    [Graphical view]
    PANTHERiPTHR10491. PTHR10491. 1 hit.
    PfamiPF04321. RmlD_sub_bind. 1 hit.
    [Graphical view]
    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_003197.1.
    WP_001023662.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL21000; AAL21000; STM2096.
    GeneIDi1253617.
    KEGGistm:STM2096.
    PATRICi32382775. VBISalEnt20916_2218.

    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_003197.1.
    WP_001023662.1. NC_003197.1.

    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...

    Protein-protein interaction databases

    STRINGi99287.STM2096.

    Proteomic databases

    PaxDbiP26392.
    PRIDEiP26392.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL21000; AAL21000; STM2096.
    GeneIDi1253617.
    KEGGistm:STM2096.
    PATRICi32382775. VBISalEnt20916_2218.

    Phylogenomic databases

    eggNOGiENOG4105DBZ. Bacteria.
    COG1091. LUCA.
    HOGENOMiHOG000227712.
    KOiK00067.
    OMAiGYASRYE.
    PhylomeDBiP26392.

    Enzyme and pathway databases

    UniPathwayiUPA00124.
    UPA00281.
    SABIO-RKP26392.

    Miscellaneous databases

    EvolutionaryTraceiP26392.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR005913. dTDP_dehydrorham_reduct.
    IPR016040. NAD(P)-bd_dom.
    IPR029903. RmlD-like-bd.
    [Graphical view]
    PANTHERiPTHR10491. PTHR10491. 1 hit.
    PfamiPF04321. RmlD_sub_bind. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01214. rmlD. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRMLD_SALTY
    AccessioniPrimary (citable) accession number: P26392
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: August 1, 1992
    Last modified: November 2, 2016
    This is version 120 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    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.