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P26394

- RMLC_SALTY

UniProt

P26394 - RMLC_SALTY

Protein

dTDP-4-dehydrorhamnose 3,5-epimerase

Gene

rfbC

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 105 (01 Oct 2014)
      Sequence version 1 (01 Aug 1992)
      Previous versions | rss
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    Functioni

    Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.1 Publication

    Catalytic activityi

    dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei24 – 241Substrate1 Publication
    Binding sitei29 – 291Substrate1 Publication
    Binding sitei48 – 481Substrate1 Publication
    Binding sitei50 – 501SubstrateBy similarity
    Binding sitei60 – 601Substrate1 Publication
    Binding sitei63 – 631SubstrateBy similarity
    Sitei63 – 631Important in abstrating the protons in C3' and C5'
    Binding sitei73 – 731SubstrateBy similarity
    Binding sitei84 – 841SubstrateBy similarity
    Binding sitei120 – 1201SubstrateBy similarity
    Sitei133 – 1331May have a key role in proton donation to C5'

    GO - Molecular functioni

    1. dTDP-4-dehydrorhamnose 3,5-epimerase 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

    Isomerase

    Keywords - Biological processi

    Lipopolysaccharide biosynthesis

    Enzyme and pathway databases

    BioCyciSENT99287:GCTI-2106-MONOMER.
    SABIO-RKP26394.
    UniPathwayiUPA00124.
    UPA00281.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dTDP-4-dehydrorhamnose 3,5-epimerase (EC:5.1.3.13)
    Alternative name(s):
    Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
    dTDP-4-keto-6-deoxyglucose 3,5-epimerase
    dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
    dTDP-L-rhamnose synthase
    Gene namesi
    Name:rfbC
    Synonyms:rmlC
    Ordered Locus Names:STM2094
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi63 – 631H → A: Loss of epimerase activity. 1 Publication
    Mutagenesisi73 – 731K → A: Reduces the epimerase activity by over 100-fold. 1 Publication
    Mutagenesisi133 – 1331Y → F: Reduces the epimerase activity by over 1000-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 183183dTDP-4-dehydrorhamnose 3,5-epimerasePRO_0000207979Add
    BLAST

    Proteomic databases

    PaxDbiP26394.
    PRIDEiP26394.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM2094.

    Structurei

    Secondary structure

    1
    183
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 64
    Beta strandi13 – 164
    Beta strandi19 – 224
    Beta strandi25 – 328
    Helixi33 – 408
    Beta strandi48 – 558
    Beta strandi58 – 658
    Helixi67 – 693
    Beta strandi73 – 8816
    Turni94 – 974
    Beta strandi99 – 1057
    Turni106 – 1083
    Beta strandi111 – 1144
    Beta strandi118 – 1247
    Beta strandi126 – 13712
    Turni141 – 1433
    Beta strandi144 – 1463
    Turni152 – 1554
    Helixi168 – 1714
    Helixi176 – 1783

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DZRX-ray2.17A/B1-183[»]
    1DZTX-ray2.20A/B1-183[»]
    ProteinModelPortaliP26394.
    SMRiP26394. Positions 1-183.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP26394.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni169 – 1702Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1898.
    HOGENOMiHOG000227724.
    KOiK01790.
    OMAiSERSIIW.
    OrthoDBiEOG6HTP2V.
    PhylomeDBiP26394.

    Family and domain databases

    Gene3Di2.60.120.10. 1 hit.
    InterProiIPR000888. dTDP_sugar_isom.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PANTHERiPTHR21047. PTHR21047. 1 hit.
    PfamiPF00908. dTDP_sugar_isom. 1 hit.
    [Graphical view]
    ProDomiPD001462. dTDP_sugar_isom. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    SUPFAMiSSF51182. SSF51182. 1 hit.
    TIGRFAMsiTIGR01221. rmlC. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P26394-1 [UniParc]FASTAAdd to Basket

    « Hide

    MMIVIKTAIP DVLILEPKVF GDERGFFFES YNQQTFEELI GRKVTFVQDN    50
    HSKSKKNVLR GLHFQRGENA QGKLVRCAVG EVFDVAVDIR KESPTFGQWV 100
    GVNLSAENKR QLWIPEGFAH GFVTLSEYAE FLYKATNYYS PSSEGSILWN 150
    DEAIGIEWPF SQLPELSAKD AAAPLLDQAL LTE 183
    Length:183
    Mass (Da):20,663
    Last modified:August 1, 1992 - v1
    Checksum:i0176B52C38038C77
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X56793 Genomic DNA. Translation: CAA40118.1.
    AE006468 Genomic DNA. Translation: AAL20998.1.
    PIRiS15302.
    RefSeqiNP_461039.1. NC_003197.1.
    WP_000973708.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL20998; AAL20998; STM2094.
    GeneIDi1253615.
    KEGGistm:STM2094.
    PATRICi32382771. VBISalEnt20916_2216.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X56793 Genomic DNA. Translation: CAA40118.1 .
    AE006468 Genomic DNA. Translation: AAL20998.1 .
    PIRi S15302.
    RefSeqi NP_461039.1. NC_003197.1.
    WP_000973708.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DZR X-ray 2.17 A/B 1-183 [» ]
    1DZT X-ray 2.20 A/B 1-183 [» ]
    ProteinModelPortali P26394.
    SMRi P26394. Positions 1-183.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM2094.

    Proteomic databases

    PaxDbi P26394.
    PRIDEi P26394.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL20998 ; AAL20998 ; STM2094 .
    GeneIDi 1253615.
    KEGGi stm:STM2094.
    PATRICi 32382771. VBISalEnt20916_2216.

    Phylogenomic databases

    eggNOGi COG1898.
    HOGENOMi HOG000227724.
    KOi K01790.
    OMAi SERSIIW.
    OrthoDBi EOG6HTP2V.
    PhylomeDBi P26394.

    Enzyme and pathway databases

    UniPathwayi UPA00124 .
    UPA00281 .
    BioCyci SENT99287:GCTI-2106-MONOMER.
    SABIO-RK P26394.

    Miscellaneous databases

    EvolutionaryTracei P26394.

    Family and domain databases

    Gene3Di 2.60.120.10. 1 hit.
    InterProi IPR000888. dTDP_sugar_isom.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view ]
    PANTHERi PTHR21047. PTHR21047. 1 hit.
    Pfami PF00908. dTDP_sugar_isom. 1 hit.
    [Graphical view ]
    ProDomi PD001462. dTDP_sugar_isom. 1 hit.
    [Graphical view ] [Entries sharing at least one domain ]
    SUPFAMi SSF51182. SSF51182. 1 hit.
    TIGRFAMsi TIGR01221. rmlC. 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. "RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation."
      Dong C., Major L.L., Srikannathasan V., Errey J.C., Giraud M.F., Lam J.S., Graninger M., Messner P., McNeil M.R., Field R.A., Whitfield C., Naismith J.H.
      J. Mol. Biol. 365:146-159(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF HIS-63; LYS-73 AND TYR-133, FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS, CATALYTIC ACTIVITY, REACTION MECHANISM.
    4. "RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase."
      Giraud M.-F., Leonard G.A., Field R.A., Berlind C., Naismith J.H.
      Nat. Struct. Biol. 7:398-402(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.17 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, SUBUNIT.

    Entry informationi

    Entry nameiRMLC_SALTY
    AccessioniPrimary (citable) accession number: P26394
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: August 1, 1992
    Last modified: October 1, 2014
    This is version 105 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