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Protein

Arabinose 5-phosphate isomerase KdsD

Gene

kdsD

Organism
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs). Catalyzes the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).1 Publication

Catalytic activityi

D-arabinose 5-phosphate = D-ribulose 5-phosphate.1 Publication

Enzyme regulationi

Inhibited by hydroxamates, mimicking the putative enediol reaction intermediate. Most potent inhibition, with an IC50 of 0.7 µM, is obtained with the 4 carbon-based hydroxamate containing acetyl moieties.1 Publication

Kineticsi

  1. KM=0.38 mM for A5P (at pH 8.5 and at 37 degrees Celsius)1 Publication

    Pathwayi: 3-deoxy-D-manno-octulosonate biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate.
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. Arabinose 5-phosphate isomerase KdsD (kdsD)
    2. 2-dehydro-3-deoxyphosphooctonate aldolase (kdsA), 2-dehydro-3-deoxyphosphooctonate aldolase (kdsA)
    3. no protein annotated in this organism
    This subpathway is part of the pathway 3-deoxy-D-manno-octulosonate biosynthesis, which is itself part of Carbohydrate biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate, the pathway 3-deoxy-D-manno-octulosonate biosynthesis and in Carbohydrate biosynthesis.

    Pathwayi: lipopolysaccharide biosynthesis

    This protein is involved in the pathway lipopolysaccharide biosynthesis, which is part of Bacterial outer membrane biogenesis.
    View all proteins of this organism that are known to be involved in the pathway lipopolysaccharide biosynthesis and in Bacterial outer membrane biogenesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei58 – 581Catalytically relevantBy similarity
    Metal bindingi81 – 811ZincBy similarity
    Binding sitei81 – 811SubstrateBy similarity
    Binding sitei87 – 871SubstrateBy similarity
    Sitei110 – 1101Catalytically relevantBy similarity
    Sitei151 – 1511Catalytically relevantBy similarity
    Sitei192 – 1921Catalytically relevantBy similarity
    Binding sitei221 – 2211SubstrateBy similarity
    Binding sitei273 – 2731SubstrateBy similarity

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Carbohydrate metabolism, Lipopolysaccharide biosynthesis

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciFTUL177416:GNBP-799-MONOMER.
    UniPathwayiUPA00030.
    UPA00357; UER00473.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Arabinose 5-phosphate isomerase KdsD (EC:5.3.1.13)
    Short name:
    API
    Gene namesi
    Name:kdsD
    Ordered Locus Names:FTT_0788c
    OrganismiFrancisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
    Taxonomic identifieri177416 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaThiotrichalesFrancisellaceaeFrancisella
    Proteomesi
    • UP000001174 Componenti: Chromosome

    Pathology & Biotechi

    Chemistry

    ChEMBLiCHEMBL1770042.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 327327Arabinose 5-phosphate isomerase KdsDPRO_0000417166Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.By similarity

    Protein-protein interaction databases

    STRINGi177416.FTT_0788c.

    Chemistry

    BindingDBiQ5NGP7.

    Structurei

    3D structure databases

    ProteinModelPortaliQ5NGP7.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini41 – 183143SISPROSITE-ProRule annotationAdd
    BLAST
    Domaini209 – 26860CBS 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini275 – 32753CBS 2PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni74 – 752Substrate bindingBy similarity
    Regioni113 – 12210Substrate bindingBy similarity
    Regioni147 – 1493Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the SIS family. GutQ/KpsF subfamily.Curated
    Contains 2 CBS domains.PROSITE-ProRule annotation
    Contains 1 SIS domain.PROSITE-ProRule annotation

    Keywords - Domaini

    CBS domain, Repeat

    Phylogenomic databases

    eggNOGiENOG4105C2X. Bacteria.
    COG0517. LUCA.
    COG0794. LUCA.
    HOGENOMiHOG000264729.
    KOiK06041.
    OMAiLMACLMR.

    Family and domain databases

    InterProiIPR000644. CBS_dom.
    IPR004800. KdsD/KpsF-type.
    IPR001347. SIS.
    [Graphical view]
    PfamiPF00571. CBS. 2 hits.
    PF01380. SIS. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004692. KdsD_KpsF. 1 hit.
    SMARTiSM00116. CBS. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00393. kpsF. 1 hit.
    PROSITEiPS51371. CBS. 2 hits.
    PS51464. SIS. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q5NGP7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEISMTSHIN NAVETFRLEI ETLEKLKNSI DENFEKACEI ILENNRDKSR
    60 70 80 90 100
    VIITGMGKSG HIGKKMAATF ASTGTPAFFV HPGEAGHGDF GMITKNDVLI
    110 120 130 140 150
    AISNSGTSSE IMGLLPMIKH LDIPIIAITS NPKSILARNS NVTLNLHVDK
    160 170 180 190 200
    EACPLNLAPT SSTTATLVLG DALAIALLKA KNFSEKDFAF SHPNGALGRK
    210 220 230 240 250
    LILKVENIMR KGNEIPIVKP TDNIRKAILE ISDKGVGNTL VAENNTLLGI
    260 270 280 290 300
    FTDGDLRRMF EAESFNSQRA ISEVMTKNPK SISKEEMAIT ALEKMEKYEI
    310 320
    TSLAVVDNGH NILGIVTMHD LIKLELR
    Length:327
    Mass (Da):35,691
    Last modified:February 1, 2005 - v1
    Checksum:i21D9D0564BAF1831
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ749949 Genomic DNA. Translation: CAG45421.1.
    RefSeqiWP_003020686.1. NC_006570.2.
    YP_169795.1. NC_006570.2.

    Genome annotation databases

    EnsemblBacteriaiCAG45421; CAG45421; FTT_0788c.
    GeneIDi3192129.
    KEGGiftu:FTT_0788c.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ749949 Genomic DNA. Translation: CAG45421.1.
    RefSeqiWP_003020686.1. NC_006570.2.
    YP_169795.1. NC_006570.2.

    3D structure databases

    ProteinModelPortaliQ5NGP7.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi177416.FTT_0788c.

    Chemistry

    BindingDBiQ5NGP7.
    ChEMBLiCHEMBL1770042.

    Protocols and materials databases

    DNASUi3192129.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAG45421; CAG45421; FTT_0788c.
    GeneIDi3192129.
    KEGGiftu:FTT_0788c.

    Phylogenomic databases

    eggNOGiENOG4105C2X. Bacteria.
    COG0517. LUCA.
    COG0794. LUCA.
    HOGENOMiHOG000264729.
    KOiK06041.
    OMAiLMACLMR.

    Enzyme and pathway databases

    UniPathwayiUPA00030.
    UPA00357; UER00473.
    BioCyciFTUL177416:GNBP-799-MONOMER.

    Family and domain databases

    InterProiIPR000644. CBS_dom.
    IPR004800. KdsD/KpsF-type.
    IPR001347. SIS.
    [Graphical view]
    PfamiPF00571. CBS. 2 hits.
    PF01380. SIS. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004692. KdsD_KpsF. 1 hit.
    SMARTiSM00116. CBS. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00393. kpsF. 1 hit.
    PROSITEiPS51371. CBS. 2 hits.
    PS51464. SIS. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiKDSD_FRATT
    AccessioniPrimary (citable) accession number: Q5NGP7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 16, 2012
    Last sequence update: February 1, 2005
    Last modified: September 7, 2016
    This is version 66 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

    Complete proteome, Reference proteome

    Documents

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

    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 one 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.