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Protein

Arabinose 5-phosphate isomerase KdsD

Gene

kdsD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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). KdsD is not essential in the KDO biosynthesis and can be substituted by GutQ. Catalyzes the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).3 Publications

Catalytic activityi

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

Enzyme regulationi

Completely inhibited by 10 µM of nickel, copper, cadmium and mercury ions. Inhibited by zinc with an IC50 of 1-3 µM. Metal ion inhibition may be a mechanism to control activity in vivo.2 Publications

Kineticsi

  1. KM=0.35 mM for Ru5P (at pH 8.5 and at 37 degrees Celsius)1 Publication
  2. KM=0.61 mM for A5P (at pH 8.5 and at 37 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 8.4.1 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)
    3. 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC (kdsC)
    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)DescriptionActionsGraphical viewLength
    Sitei59Catalytically relevant1
    Metal bindingi82ZincBy similarity1
    Binding sitei82SubstrateBy similarity1
    Binding sitei88SubstrateBy similarity1
    Sitei111Catalytically relevant1
    Sitei152Catalytically relevant1
    Sitei193Catalytically relevant1
    Binding sitei222SubstrateBy similarity1
    Binding sitei275SubstrateBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    • keto-3-deoxy-D-manno-octulosonic acid biosynthetic process Source: EcoCyc

    Keywordsi

    Molecular functionIsomerase
    Biological processCarbohydrate metabolism, Lipopolysaccharide biosynthesis
    LigandMetal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:G7662-MONOMER
    MetaCyc:G7662-MONOMER
    BRENDAi5.3.1.13 2026
    UniPathwayiUPA00030
    UPA00357; UER00473

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Arabinose 5-phosphate isomerase KdsD (EC:5.3.1.13)
    Short name:
    API
    Short name:
    L-API
    Gene namesi
    Name:kdsD
    Synonyms:yrbH
    Ordered Locus Names:b3197, JW3164
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12803 kdsD

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi59K → A: Inactive. 1 Publication1
    Mutagenesisi88H → A: Shows 9.5% of residual activity compared to the wild-type. 1 Publication1
    Mutagenesisi111E → A: Shows 62% of residual activity compared to the wild-type. 1 Publication1
    Mutagenesisi152E → A: Shows 19% of residual activity compared to the wild-type. It is able to support growth. 1 Publication1
    Mutagenesisi193H → A: Inactive. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001365751 – 328Arabinose 5-phosphate isomerase KdsDAdd BLAST328

    Proteomic databases

    PaxDbiP45395
    PRIDEiP45395

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Protein-protein interaction databases

    BioGridi4259369339 interactors.
    DIPiDIP-12910N
    IntActiP45395 9 interactors.
    STRINGi316385.ECDH10B_3371

    Structurei

    Secondary structure

    1328
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi12 – 27Combined sources16
    Helixi28 – 32Combined sources5
    Helixi36 – 46Combined sources11
    Beta strandi52 – 56Combined sources5
    Helixi58 – 72Combined sources15
    Turni73 – 75Combined sources3
    Beta strandi78 – 80Combined sources3
    Helixi85 – 89Combined sources5
    Beta strandi99 – 103Combined sources5
    Beta strandi105 – 107Combined sources3
    Helixi110 – 120Combined sources11
    Turni121 – 123Combined sources3
    Beta strandi126 – 131Combined sources6
    Helixi136 – 140Combined sources5
    Beta strandi141 – 146Combined sources6
    Helixi162 – 182Combined sources21

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2XHZX-ray2.60A/B/C/D1-183[»]
    ProteinModelPortaliP45395
    SMRiP45395
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45395

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini42 – 184SISPROSITE-ProRule annotationAdd BLAST143
    Domaini210 – 268CBS 1PROSITE-ProRule annotationAdd BLAST59
    Domaini277 – 328CBS 2PROSITE-ProRule annotationAdd BLAST52

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni75 – 76Substrate bindingBy similarity2
    Regioni114 – 123Substrate bindingBy similarity10
    Regioni148 – 150Substrate bindingBy similarity3

    Sequence similaritiesi

    Belongs to the SIS family. GutQ/KpsF subfamily.Curated

    Keywords - Domaini

    CBS domain, Repeat

    Phylogenomic databases

    eggNOGiENOG4105C2X Bacteria
    COG0517 LUCA
    COG0794 LUCA
    HOGENOMiHOG000264729
    InParanoidiP45395
    KOiK06041
    OMAiFMHAADA
    PhylomeDBiP45395

    Family and domain databases

    CDDicd05014 SIS_Kpsf, 1 hit
    InterProiView protein in InterPro
    IPR000644 CBS_dom
    IPR004800 KdsD/KpsF-type
    IPR001347 SIS
    IPR035474 SIS_Kpsf
    PfamiView protein in Pfam
    PF00571 CBS, 2 hits
    PF01380 SIS, 1 hit
    PIRSFiPIRSF004692 KdsD_KpsF, 1 hit
    TIGRFAMsiTIGR00393 kpsF, 1 hit
    PROSITEiView protein in PROSITE
    PS51371 CBS, 2 hits
    PS51464 SIS, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P45395-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSHVELQPGF DFQQAGKEVL AIERECLAEL DQYINQNFTL ACEKMFWCKG
    60 70 80 90 100
    KVVVMGMGKS GHIGRKMAAT FASTGTPSFF VHPGEAAHGD LGMVTPQDVV
    110 120 130 140 150
    IAISNSGESS EITALIPVLK RLHVPLICIT GRPESSMARA ADVHLCVKVA
    160 170 180 190 200
    KEACPLGLAP TSSTTATLVM GDALAVALLK ARGFTAEDFA LSHPGGALGR
    210 220 230 240 250
    KLLLRVNDIM HTGDEIPHVK KTASLRDALL EVTRKNLGMT VICDDNMMIE
    260 270 280 290 300
    GIFTDGDLRR VFDMGVDVRQ LSIADVMTPG GIRVRPGILA VEALNLMQSR
    310 320
    HITSVMVADG DHLLGVLHMH DLLRAGVV
    Length:328
    Mass (Da):35,196
    Last modified:November 1, 1995 - v1
    Checksum:iB2BE546C8F56C1B4
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA Translation: AAA57998.1
    U00096 Genomic DNA Translation: AAC76229.1
    AP009048 Genomic DNA Translation: BAE77241.1
    PIRiG65110
    RefSeqiNP_417664.1, NC_000913.3
    WP_001295557.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC76229; AAC76229; b3197
    BAE77241; BAE77241; BAE77241
    GeneIDi947734
    KEGGiecj:JW3164
    eco:b3197
    PATRICifig|1411691.4.peg.3534

    Similar proteinsi

    Entry informationi

    Entry nameiKDSD_ECOLI
    AccessioniPrimary (citable) accession number: P45395
    Secondary accession number(s): Q2M915
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: March 28, 2018
    This is version 122 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome