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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

    Pathway:idTDP-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.

    Pathway:iLPS 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei12 – 121NAD; via amide nitrogen
    Binding sitei102 – 1021NADP; via carbonyl oxygen
    Binding sitei153 – 1531Substrate; via amide nitrogen
    Binding sitei154 – 1541NAD; via amide nitrogen
    Binding sitei223 – 2231Substrate
    Binding sitei260 – 2601Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi7 – 115NAD
    Nucleotide bindingi11 – 122NADP
    Nucleotide bindingi30 – 312NAD
    Nucleotide bindingi39 – 402NAD/NADP
    Nucleotide bindingi62 – 654NAD
    Nucleotide bindingi63 – 653NADP
    Nucleotide bindingi128 – 1325NAD/NADP

    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

    BioCyciRETL1328306-WGS:GSTH-1528-MONOMER.
    SENT99287:GCTI-2108-MONOMER.
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi67 – 671V → A: Significantly reduces enzyme activity. 1 Publication
    Mutagenesisi68 – 681D → A: Slightly reduces enzyme activity. 1 Publication
    Mutagenesisi104 – 1041T → A: Loss of activity. 1 Publication
    Mutagenesisi128 – 1281Y → F: Loss of activity. 1 Publication
    Mutagenesisi153 – 1531W → A: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 299299dTDP-4-dehydrorhamnose reductasePRO_0000207986Add
    BLAST

    Proteomic databases

    PaxDbiP26392.
    PRIDEiP26392.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM2096.

    Structurei

    Secondary structure

    1
    299
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 65Combined sources
    Helixi11 – 199Combined sources
    Turni20 – 234Combined sources
    Beta strandi24 – 296Combined sources
    Beta strandi34 – 363Combined sources
    Helixi43 – 5311Combined sources
    Beta strandi56 – 605Combined sources
    Helixi67 – 704Combined sources
    Helixi74 – 818Combined sources
    Helixi83 – 9210Combined sources
    Turni93 – 964Combined sources
    Beta strandi98 – 1047Combined sources
    Helixi105 – 1073Combined sources
    Beta strandi112 – 1143Combined sources
    Helixi127 – 14216Combined sources
    Beta strandi144 – 1518Combined sources
    Beta strandi153 – 1553Combined sources
    Beta strandi157 – 1593Combined sources
    Helixi162 – 17211Combined sources
    Beta strandi174 – 1796Combined sources
    Helixi189 – 20517Combined sources
    Helixi207 – 2093Combined sources
    Beta strandi211 – 2144Combined sources
    Helixi223 – 23715Combined sources
    Beta strandi245 – 2495Combined sources
    Helixi251 – 2533Combined sources
    Beta strandi262 – 2643Combined sources
    Helixi269 – 2757Combined sources
    Helixi282 – 29413Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KBZX-ray2.20A1-299[»]
    1KC1X-ray2.60A1-299[»]
    1KC3X-ray2.70A1-299[»]
    1N2SX-ray2.00A1-299[»]
    ProteinModelPortaliP26392.
    SMRiP26392. Positions 1-298.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP26392.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni104 – 1052Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1091.
    HOGENOMiHOG000227712.
    KOiK00067.
    OMAiPYWRDSL.
    OrthoDBiEOG6HTP2V.
    PhylomeDBiP26392.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR005913. dTDP_dehydrorham_reduct.
    IPR016040. NAD(P)-bd_dom.
    IPR029900. RmlD.
    IPR029903. RmlD-like-bd.
    [Graphical view]
    PANTHERiPTHR10491. PTHR10491. 1 hit.
    PTHR10491:SF5. PTHR10491:SF5. 1 hit.
    PfamiPF04321. RmlD_sub_bind. 1 hit.
    [Graphical view]
    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KBZX-ray2.20A1-299[»]
    1KC1X-ray2.60A1-299[»]
    1KC3X-ray2.70A1-299[»]
    1N2SX-ray2.00A1-299[»]
    ProteinModelPortaliP26392.
    SMRiP26392. Positions 1-298.
    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

    eggNOGiCOG1091.
    HOGENOMiHOG000227712.
    KOiK00067.
    OMAiPYWRDSL.
    OrthoDBiEOG6HTP2V.
    PhylomeDBiP26392.

    Enzyme and pathway databases

    UniPathwayiUPA00124.
    UPA00281.
    BioCyciRETL1328306-WGS:GSTH-1528-MONOMER.
    SENT99287:GCTI-2108-MONOMER.
    SABIO-RKP26392.

    Miscellaneous databases

    EvolutionaryTraceiP26392.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR005913. dTDP_dehydrorham_reduct.
    IPR016040. NAD(P)-bd_dom.
    IPR029900. RmlD.
    IPR029903. RmlD-like-bd.
    [Graphical view]
    PANTHERiPTHR10491. PTHR10491. 1 hit.
    PTHR10491:SF5. PTHR10491:SF5. 1 hit.
    PfamiPF04321. RmlD_sub_bind. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01214. rmlD. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Structure and sequence of the rfb (O antigen) gene cluster of Salmonella serovar typhimurium (strain LT2)."
      Jiang X.-M., Neal B., Santiago F., Lee S.J., Romana L.K., Reeves P.R.
      Mol. Microbiol. 5:695-713(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: LT2.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    3. "Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode."
      Blankenfeldt W., Kerr I.D., Giraud M.F., McMiken H.J., Leonard G., Whitfield C., Messner P., Graninger M., Naismith J.H.
      Structure 10:773-786(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH NADH, NADPH AND DTDP-L-RHAMNOSE, FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF VAL-67; ASP-68; THR-104; TYR-128 AND TRP-153, SUBUNIT, COFACTOR, REACTION MECHANISM.

    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: July 22, 2015
    This is version 113 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

    External Data

    Dasty 3

    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 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.