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P37778

- RMLD_SHIFL

UniProt

P37778 - RMLD_SHIFL

Protein

dTDP-4-dehydrorhamnose reductase

Gene

rfbD

Organism
Shigella flexneri
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 102 (01 Oct 2014)
      Sequence version 2 (10 Jan 2003)
      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.

    Cofactori

    Binds 1 magnesium ion per monomer.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei12 – 121NAD; via amide nitrogenBy similarity
    Binding sitei102 – 1021NADP; via carbonyl oxygenBy similarity
    Binding sitei153 – 1531Substrate; via amide nitrogenBy similarity
    Binding sitei154 – 1541NAD; via amide nitrogenBy similarity
    Binding sitei223 – 2231SubstrateBy similarity
    Binding sitei260 – 2601SubstrateBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi7 – 137NADPSequence Analysis
    Nucleotide bindingi7 – 115NADBy similarity
    Nucleotide bindingi11 – 122NADPBy similarity
    Nucleotide bindingi30 – 312NADBy similarity
    Nucleotide bindingi39 – 402NAD/NADPBy similarity
    Nucleotide bindingi62 – 654NADBy similarity
    Nucleotide bindingi63 – 653NADPBy similarity
    Nucleotide bindingi128 – 1325NAD/NADPBy similarity

    GO - Molecular functioni

    1. dTDP-4-dehydrorhamnose reductase activity Source: UniProtKB

    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

    NADP

    Enzyme and pathway databases

    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
    Ordered Locus Names:SF2103, S2226
    OrganismiShigella flexneri
    Taxonomic identifieri623 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
    ProteomesiUP000001006: Chromosome, UP000002673: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 299299dTDP-4-dehydrorhamnose reductasePRO_0000207987Add
    BLAST

    Proteomic databases

    PaxDbiP37778.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    STRINGi198214.SF2103.

    Structurei

    3D structure databases

    ProteinModelPortaliP37778.
    SMRiP37778. Positions 1-297.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

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

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1091.
    HOGENOMiHOG000227712.
    KOiK00067.
    OMAiETTWHGY.
    OrthoDBiEOG6HTP2V.

    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.

    P37778-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNILLFGKTG QVGWELQRAL APLGNLIALD VHSTDYCGDF SNPEGVAETV    50
    KKIRPDVIVN AAAHTAVDKA ESEPNFAQLL NATCVEAIAK AANEVGAWVI 100
    HYSTDYVFPG NGDTPWLETD ATAPLNVYGE TKLAGEKALQ EHCAKHLIFR 150
    TSWVYAGKGN NFAKTMLRLA KEREELAVIN DQFGAPTGAE LLADCTAHAI 200
    RVAANKPEVA GLYHLVAGGT TTWHDYAALV FEEARRAGIN LALNKLNAVP 250
    TTAYPTPARR PHNSRLNTEK FQQNFALVLP DWQVGVKRML NELFTTTAI 299
    Length:299
    Mass (Da):32,565
    Last modified:January 10, 2003 - v2
    Checksum:iF2C6EF7BA8BD54DE
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti89 – 891A → I in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti115 – 1151P → A in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti130 – 1301E → G in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti135 – 1362GE → WG in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti141 – 1411E → D in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti144 – 1441A → G in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti172 – 1721E → D in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti175 – 1751E → T in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti180 – 1801N → T in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti190 – 1901E → LD in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti197 – 1971A → R in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti201 – 2022RV → WL in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti227 – 2271A → P in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti232 – 2321E → K in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti239 – 2391I → F in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti242 – 2421A → P in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti260 – 2601R → G in CAA50768. (PubMed:8170390)Curated
    Sequence conflicti264 – 2641S → F in CAA50768. (PubMed:8170390)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X71970 Genomic DNA. Translation: CAA50768.1.
    L14842 Genomic DNA. Translation: AAA53680.1.
    AE005674 Genomic DNA. Translation: AAN43642.1.
    AE014073 Genomic DNA. Translation: AAP17471.1.
    PIRiC55213.
    S41535.
    RefSeqiNP_707935.1. NC_004337.2.
    NP_837662.1. NC_004741.1.

    Genome annotation databases

    EnsemblBacteriaiAAN43642; AAN43642; SF2103.
    AAP17471; AAP17471; S2226.
    GeneIDi1025316.
    1078509.
    KEGGisfl:SF2103.
    sfx:S2226.
    PATRICi18705959. VBIShiFle31049_2458.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X71970 Genomic DNA. Translation: CAA50768.1 .
    L14842 Genomic DNA. Translation: AAA53680.1 .
    AE005674 Genomic DNA. Translation: AAN43642.1 .
    AE014073 Genomic DNA. Translation: AAP17471.1 .
    PIRi C55213.
    S41535.
    RefSeqi NP_707935.1. NC_004337.2.
    NP_837662.1. NC_004741.1.

    3D structure databases

    ProteinModelPortali P37778.
    SMRi P37778. Positions 1-297.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 198214.SF2103.

    Proteomic databases

    PaxDbi P37778.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAN43642 ; AAN43642 ; SF2103 .
    AAP17471 ; AAP17471 ; S2226 .
    GeneIDi 1025316.
    1078509.
    KEGGi sfl:SF2103.
    sfx:S2226.
    PATRICi 18705959. VBIShiFle31049_2458.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00124 .
    UPA00281 .

    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. "Characterization of the dTDP-rhamnose biosynthetic genes encoded in the rfb locus of Shigella flexneri."
      Macpherson D.F., Manning P.A., Morona R.
      Mol. Microbiol. 11:281-292(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS.
      Strain: PE577 / Serotype 2a.
    2. "Nucleotide sequence of the rhamnose biosynthetic operon of Shigella flexneri 2a and role of lipopolysaccharide in virulence."
      Rajakumar K., Jost B.H., Sasakawa C., Okada N., Yoshikawa M., Adler B.
      J. Bacteriol. 176:2362-2373(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: YSH6200 / Serotype 2a.
    3. "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157."
      Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y.
      , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.
      Nucleic Acids Res. 30:4432-4441(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 301 / Serotype 2a.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700930 / 2457T / Serotype 2a.

    Entry informationi

    Entry nameiRMLD_SHIFL
    AccessioniPrimary (citable) accession number: P37778
    Secondary accession number(s): Q54163
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: January 10, 2003
    Last modified: October 1, 2014
    This is version 102 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3