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P26392

- RMLD_SALTY

UniProt

P26392 - RMLD_SALTY

Protein

dTDP-4-dehydrorhamnose reductase

Gene

rfbD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 1 (01 Aug 1992)
      Previous versions | rss
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    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

    Binds 1 magnesium ion per monomer.1 Publication

    Kineticsi

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

    Pathwayi

    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

    1. dTDP-4-dehydrorhamnose reductase activity Source: UniProtKB
    2. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. dTDP-rhamnose biosynthetic process Source: UniProtKB-UniPathway
    2. extracellular polysaccharide biosynthetic process Source: UniProtKB
    3. lipopolysaccharide biosynthetic process Source: UniProtKB
    4. O antigen biosynthetic process Source: UniProtKB-UniPathway

    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: 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 – 65
    Helixi11 – 199
    Turni20 – 234
    Beta strandi24 – 296
    Beta strandi34 – 363
    Helixi43 – 5311
    Beta strandi56 – 605
    Helixi67 – 704
    Helixi74 – 818
    Helixi83 – 9210
    Turni93 – 964
    Beta strandi98 – 1047
    Helixi105 – 1073
    Beta strandi112 – 1143
    Helixi127 – 14216
    Beta strandi144 – 1518
    Beta strandi153 – 1553
    Beta strandi157 – 1593
    Helixi162 – 17211
    Beta strandi174 – 1796
    Helixi189 – 20517
    Helixi207 – 2093
    Beta strandi211 – 2144
    Helixi223 – 23715
    Beta strandi245 – 2495
    Helixi251 – 2533
    Beta strandi262 – 2643
    Helixi269 – 2757
    Helixi282 – 29413

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    OMAiETTWHGY.
    OrthoDBiEOG6HTP2V.
    PhylomeDBiP26392.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR005913. dTDP_dehydrorham_reduct.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF04321. RmlD_sub_bind. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01214. rmlD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P26392-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNILLFGKTG QVGWELQRSL APVGNLIALD VHSKEFCGDF SNPKGVAETV    50
    RKLRPDVIVN AAAHTAVDKA ESEPELAQLL NATSVEAIAK AANETGAWVV 100
    HYSTDYVFPG TGDIPWQETD ATSPLNVYGK TKLAGEKALQ DNCPKHLIFR 150
    TSWVYAGKGN NFAKTMLRLA KERQTLSVIN DQYGAPTGAE LLADCTAHAI 200
    RVALNKPEVA GLYHLVAGGT TTWHDYAALV FDEARKAGIT LALTELNAVP 250
    TSAYPTPASR PGNSRLNTEK FQRNFDLILP QWELGVKRML TEMFTTTTI 299
    Length:299
    Mass (Da):32,554
    Last modified:August 1, 1992 - v1
    Checksum:iABAA0476AF5ECDE7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X56793 Genomic DNA. Translation: CAA40116.1 .
    AE006468 Genomic DNA. Translation: AAL21000.1 .
    PIRi S15300.
    RefSeqi NP_461041.1. NC_003197.1.
    WP_001023662.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1KBZ X-ray 2.20 A 1-299 [» ]
    1KC1 X-ray 2.60 A 1-299 [» ]
    1KC3 X-ray 2.70 A 1-299 [» ]
    1N2S X-ray 2.00 A 1-299 [» ]
    ProteinModelPortali P26392.
    SMRi P26392. Positions 1-298.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM2096.

    Proteomic databases

    PaxDbi P26392.
    PRIDEi P26392.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL21000 ; AAL21000 ; STM2096 .
    GeneIDi 1253617.
    KEGGi stm:STM2096.
    PATRICi 32382775. VBISalEnt20916_2218.

    Phylogenomic databases

    eggNOGi COG1091.
    HOGENOMi HOG000227712.
    KOi K00067.
    OMAi ETTWHGY.
    OrthoDBi EOG6HTP2V.
    PhylomeDBi P26392.

    Enzyme and pathway databases

    UniPathwayi UPA00124 .
    UPA00281 .
    BioCyci RETL1328306-WGS:GSTH-1528-MONOMER.
    SENT99287:GCTI-2108-MONOMER.
    SABIO-RK P26392.

    Miscellaneous databases

    EvolutionaryTracei P26392.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    InterProi IPR005913. dTDP_dehydrorham_reduct.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    Pfami PF04321. RmlD_sub_bind. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01214. rmlD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 108 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