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P26391

- RMLB_SALTY

UniProt

P26391 - RMLB_SALTY

Protein

dTDP-glucose 4,6-dehydratase

Gene

rfbB

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 112 (01 Oct 2014)
      Sequence version 1 (01 Aug 1992)
      Previous versions | rss
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    Functioni

    Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction.1 Publication

    Catalytic activityi

    dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O.1 Publication

    Cofactori

    Binds 1 NAD per subunit.2 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei80 – 801NAD; via carbonyl oxygen2 Publications
    Binding sitei84 – 841Substrate; via carbonyl oxygen1 Publication
    Binding sitei99 – 991NAD2 Publications
    Active sitei134 – 1341Proton donor1 Publication
    Active sitei135 – 1351Proton acceptor1 Publication
    Active sitei167 – 1671Proton acceptor1 Publication
    Binding sitei196 – 1961Substrate1 Publication
    Binding sitei197 – 1971NAD; via amide nitrogen2 Publications
    Binding sitei231 – 2311Substrate1 Publication
    Binding sitei266 – 2661Substrate1 Publication
    Binding sitei357 – 3571Substrate1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi10 – 123NAD2 Publications
    Nucleotide bindingi32 – 354NAD2 Publications
    Nucleotide bindingi58 – 592NAD2 Publications
    Nucleotide bindingi167 – 1715NAD2 Publications

    GO - Molecular functioni

    1. dTDP-glucose 4,6-dehydratase activity Source: UniProtKB
    2. NADH binding 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

    Lyase

    Keywords - Biological processi

    Lipopolysaccharide biosynthesis

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciSENT99287:GCTI-2109-MONOMER.
    UniPathwayiUPA00124.
    UPA00281.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dTDP-glucose 4,6-dehydratase (EC:4.2.1.46)
    Gene namesi
    Name:rfbB
    Ordered Locus Names:STM2097
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 361361dTDP-glucose 4,6-dehydratasePRO_0000183243Add
    BLAST

    Proteomic databases

    PaxDbiP26391.
    PRIDEiP26391.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi99287.STM2097.

    Structurei

    Secondary structure

    1
    361
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76
    Helixi11 – 2313
    Beta strandi27 – 326
    Helixi40 – 434
    Turni44 – 485
    Beta strandi52 – 565
    Helixi62 – 7211
    Beta strandi75 – 795
    Helixi86 – 916
    Helixi94 – 1007
    Helixi102 – 11615
    Helixi120 – 1256
    Beta strandi127 – 1337
    Helixi134 – 1374
    Helixi143 – 1453
    Helixi166 – 18520
    Beta strandi189 – 1946
    Beta strandi196 – 1994
    Helixi207 – 21711
    Beta strandi221 – 2244
    Beta strandi230 – 2356
    Helixi236 – 24914
    Beta strandi255 – 2584
    Beta strandi263 – 2653
    Helixi266 – 28015
    Helixi287 – 2904
    Beta strandi291 – 2944
    Helixi309 – 3157
    Helixi323 – 33614
    Helixi338 – 3436
    Helixi347 – 35711

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1G1AX-ray2.47A/B/C/D1-361[»]
    1KEUX-ray2.40A/B1-361[»]
    1KEWX-ray1.80A/B1-361[»]
    ProteinModelPortaliP26391.
    SMRiP26391. Positions 1-361.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP26391.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni133 – 1353Substrate binding
    Regioni206 – 2072Substrate binding
    Regioni222 – 2243Substrate binding
    Regioni297 – 3004Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1088.
    HOGENOMiHOG000168006.
    KOiK01710.
    OMAiDSERYAF.
    OrthoDBiEOG6PZXCX.
    PhylomeDBiP26391.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR005888. dTDP_Gluc_deHydtase.
    IPR001509. Epimerase_deHydtase.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR10366:SF41. PTHR10366:SF41. 1 hit.
    PfamiPF01370. Epimerase. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01181. dTDP_gluc_dehyt. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P26391-1 [UniParc]FASTAAdd to Basket

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    MKILITGGAG FIGSAVVRHI IKNTQDTVVN IDKLTYAGNL ESLSDISESN    50
    RYNFEHADIC DSAEITRIFE QYQPDAVMHL AAESHVDRSI TGPAAFIETN 100
    IVGTYALLEV ARKYWSALGE DKKNNFRFHH ISTDEVYGDL PHPDEVENSV 150
    TLPLFTETTA YAPSSPYSAS KASSDHLVRA WRRTYGLPTI VTNCSNNYGP 200
    YHFPEKLIPL VILNALEGKP LPIYGKGDQI RDWLYVEDHA RALHMVVTEG 250
    KAGETYNIGG HNEKKNLDVV FTICDLLDEI VPKATSYREQ ITYVADRPGH 300
    DRRYAIDAGK ISRELGWKPL ETFESGIRKT VEWYLANTQW VNNVKSGAYQ 350
    SWIEQNYEGR Q 361
    Length:361
    Mass (Da):40,719
    Last modified:August 1, 1992 - v1
    Checksum:i3A574B4D917EBC57
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X56793 Genomic DNA. Translation: CAA40115.1.
    AE006468 Genomic DNA. Translation: AAL21001.1.
    PIRiS15299.
    RefSeqiNP_461042.1. NC_003197.1.
    WP_000697840.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL21001; AAL21001; STM2097.
    GeneIDi1253618.
    KEGGistm:STM2097.
    PATRICi32382777. VBISalEnt20916_2219.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X56793 Genomic DNA. Translation: CAA40115.1 .
    AE006468 Genomic DNA. Translation: AAL21001.1 .
    PIRi S15299.
    RefSeqi NP_461042.1. NC_003197.1.
    WP_000697840.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1G1A X-ray 2.47 A/B/C/D 1-361 [» ]
    1KEU X-ray 2.40 A/B 1-361 [» ]
    1KEW X-ray 1.80 A/B 1-361 [» ]
    ProteinModelPortali P26391.
    SMRi P26391. Positions 1-361.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM2097.

    Proteomic databases

    PaxDbi P26391.
    PRIDEi P26391.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL21001 ; AAL21001 ; STM2097 .
    GeneIDi 1253618.
    KEGGi stm:STM2097.
    PATRICi 32382777. VBISalEnt20916_2219.

    Phylogenomic databases

    eggNOGi COG1088.
    HOGENOMi HOG000168006.
    KOi K01710.
    OMAi DSERYAF.
    OrthoDBi EOG6PZXCX.
    PhylomeDBi P26391.

    Enzyme and pathway databases

    UniPathwayi UPA00124 .
    UPA00281 .
    BioCyci SENT99287:GCTI-2109-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P26391.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    InterProi IPR005888. dTDP_Gluc_deHydtase.
    IPR001509. Epimerase_deHydtase.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    PANTHERi PTHR10366:SF41. PTHR10366:SF41. 1 hit.
    Pfami PF01370. Epimerase. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01181. dTDP_gluc_dehyt. 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. "The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway."
      Allard S.T., Giraud M.F., Whitfield C., Graninger M., Messner P., Naismith J.H.
      J. Mol. Biol. 307:283-295(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.47 ANGSTROMS) IN COMPLEX WITH NAD, COFACTOR, SUBUNIT.
    4. Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND NAD, FUNCTION AS A DEHYDRATASE, CATALYTIC ACTIVITY, COFACTOR, ACTIVE SITE, REACTION MECHANISM, SUBUNIT.

    Entry informationi

    Entry nameiRMLB_SALTY
    AccessioniPrimary (citable) accession number: P26391
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: August 1, 1992
    Last modified: October 1, 2014
    This is version 112 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