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Protein

Arabinose 5-phosphate isomerase KdsD

Gene

kdsD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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). 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)LengthDescriptionGraphical viewFeature identifierActions
    Sitei59 – 591Catalytically relevant
    Metal bindingi82 – 821ZincBy similarity
    Binding sitei82 – 821SubstrateBy similarity
    Binding sitei88 – 881SubstrateBy similarity
    Sitei111 – 1111Catalytically relevant
    Sitei152 – 1521Catalytically relevant
    Sitei193 – 1931Catalytically relevant
    Binding sitei222 – 2221SubstrateBy similarity
    Binding sitei275 – 2751SubstrateBy similarity

    GO - Molecular functioni

    • arabinose-5-phosphate isomerase activity Source: EcoCyc
    • carbohydrate binding Source: InterPro
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    • keto-3-deoxy-D-manno-octulosonic acid biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Carbohydrate metabolism, Lipopolysaccharide biosynthesis

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:G7662-MONOMER.
    ECOL316407:JW3164-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12803. kdsD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi59 – 591K → A: Inactive. 1 Publication
    Mutagenesisi88 – 881H → A: Shows 9.5% of residual activity compared to the wild-type. 1 Publication
    Mutagenesisi111 – 1111E → A: Shows 62% of residual activity compared to the wild-type. 1 Publication
    Mutagenesisi152 – 1521E → A: Shows 19% of residual activity compared to the wild-type. It is able to support growth. 1 Publication
    Mutagenesisi193 – 1931H → A: Inactive. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 328328Arabinose 5-phosphate isomerase KdsDPRO_0000136575Add
    BLAST

    Proteomic databases

    PaxDbiP45395.
    PRIDEiP45395.

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Protein-protein interaction databases

    BioGridi4259369. 336 interactions.
    DIPiDIP-12910N.
    IntActiP45395. 9 interactions.
    STRINGi511145.b3197.

    Structurei

    Secondary structure

    1
    328
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi12 – 2716Combined sources
    Helixi28 – 325Combined sources
    Helixi36 – 4611Combined sources
    Beta strandi52 – 565Combined sources
    Helixi58 – 7215Combined sources
    Turni73 – 753Combined sources
    Beta strandi78 – 803Combined sources
    Helixi85 – 895Combined sources
    Beta strandi99 – 1035Combined sources
    Beta strandi105 – 1073Combined sources
    Helixi110 – 12011Combined sources
    Turni121 – 1233Combined sources
    Beta strandi126 – 1316Combined sources
    Helixi136 – 1405Combined sources
    Beta strandi141 – 1466Combined sources
    Helixi162 – 18221Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2XHZX-ray2.60A/B/C/D1-183[»]
    ProteinModelPortaliP45395.
    SMRiP45395. Positions 10-183, 199-324.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45395.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini42 – 184143SISPROSITE-ProRule annotationAdd
    BLAST
    Domaini210 – 26859CBS 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini277 – 32852CBS 2PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni75 – 762Substrate bindingBy similarity
    Regioni114 – 12310Substrate bindingBy similarity
    Regioni148 – 1503Substrate 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.
    InParanoidiP45395.
    KOiK06041.
    OMAiLMACLMR.
    OrthoDBiEOG6RFZWS.
    PhylomeDBiP45395.

    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.
    TIGRFAMsiTIGR00393. kpsF. 1 hit.
    PROSITEiPS51371. CBS. 2 hits.
    PS51464. SIS. 1 hit.
    [Graphical view]

    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.
    PATRICi32121814. VBIEscCol129921_3291.

    Cross-referencesi

    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2XHZX-ray2.60A/B/C/D1-183[»]
    ProteinModelPortaliP45395.
    SMRiP45395. Positions 10-183, 199-324.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259369. 336 interactions.
    DIPiDIP-12910N.
    IntActiP45395. 9 interactions.
    STRINGi511145.b3197.

    Proteomic databases

    PaxDbiP45395.
    PRIDEiP45395.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76229; AAC76229; b3197.
    BAE77241; BAE77241; BAE77241.
    GeneIDi947734.
    KEGGiecj:JW3164.
    eco:b3197.
    PATRICi32121814. VBIEscCol129921_3291.

    Organism-specific databases

    EchoBASEiEB2655.
    EcoGeneiEG12803. kdsD.

    Phylogenomic databases

    eggNOGiENOG4105C2X. Bacteria.
    COG0517. LUCA.
    COG0794. LUCA.
    HOGENOMiHOG000264729.
    InParanoidiP45395.
    KOiK06041.
    OMAiLMACLMR.
    OrthoDBiEOG6RFZWS.
    PhylomeDBiP45395.

    Enzyme and pathway databases

    UniPathwayiUPA00030.
    UPA00357; UER00473.
    BioCyciEcoCyc:G7662-MONOMER.
    ECOL316407:JW3164-MONOMER.
    MetaCyc:G7662-MONOMER.
    BRENDAi5.3.1.13. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP45395.
    PROiP45395.

    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.
    TIGRFAMsiTIGR00393. kpsF. 1 hit.
    PROSITEiPS51371. CBS. 2 hits.
    PS51464. SIS. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. "Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase."
      Meredith T.C., Woodard R.W.
      J. Biol. Chem. 278:32771-32777(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A ARABINOSE 5-PHOSPHATE ISOMERASE AND IN LIPOPOLYSACCHARIDE BIOSYNTHESIS, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.
      Strain: K12.
    4. "Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate isomerase."
      Meredith T.C., Woodard R.W.
      J. Bacteriol. 187:6936-6942(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A ARABINOSE 5-PHOSPHATE ISOMERASE, NOMENCLATURE.
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG-yhbG locus."
      Sperandeo P., Pozzi C., Deho G., Polissi A.
      Res. Microbiol. 157:547-558(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN KDO BIOSYNTHESIS.
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Structure prediction and functional analysis of KdsD, an enzyme involved in lipopolysaccharide biosynthesis."
      Sommaruga S., Gioia L.D., Tortora P., Polissi A.
      Biochem. Biophys. Res. Commun. 388:222-227(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-59; GLU-111; GLU-152 AND HIS-193.
      Strain: K12.
    7. "Targeting bacterial membranes: NMR spectroscopy characterization of substrate recognition and binding requirements of D-arabinose-5-phosphate isomerase."
      Airoldi C., Sommaruga S., Merlo S., Sperandeo P., Cipolla L., Polissi A., Nicotra F.
      Chemistry 16:1897-1902(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: REACTION MECHANISM, ENZYME REGULATION.
      Strain: K12.
    8. "Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography."
      Gourlay L.J., Sommaruga S., Nardini M., Sperandeo P., Deho G., Polissi A., Bolognesi M.
      Protein Sci. 19:2430-2439(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-183 OF MUTANT ALA-59, MUTAGENESIS OF HIS-88, SUBUNIT.
      Strain: K12.

    Entry informationi

    Entry nameiKDSD_ECOLI
    AccessioniPrimary (citable) accession number: P45395
    Secondary accession number(s): Q2M915
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: May 11, 2016
    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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.