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Protein

L-fuconate dehydratase

Gene

XCC4069

Organism
Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a role in the catabolism of L-fucose. Catalyzes the dehydration of L-fuconate to 2-keto-3-deoxy-L-fuconate by the abstraction of the 2-proton to generate an enediolate intermediate that is stabilized by the magnesium ion. L-fuconate is the preferred substrate with 15-fold lower activity observed for L-galactonate and 8-fold lower activity with D-arabinonate. No activity detected with D-fuconate. Can also catalyze the epimerization of L-talonate and D-ribonate, but at slow rates.1 Publication

Catalytic activityi

L-fuconate = 2-dehydro-3-deoxy-L-fuconate + H2O.1 Publication

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Kineticsi

  1. KM=0.03 mM for L-fuconate1 Publication
  2. KM=6.2 mM for L-galactonate1 Publication
  3. KM=2.1 mM for D-arabinonate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei32 – 321Substrate1 Publication
    Binding sitei218 – 2181Substrate1 Publication
    Active sitei220 – 2201Proton donor/acceptor1 Publication
    Metal bindingi248 – 2481Magnesium2 Publications
    Binding sitei250 – 2501Substrate1 Publication
    Metal bindingi274 – 2741Magnesium2 Publications
    Binding sitei274 – 2741Substrate1 Publication
    Metal bindingi301 – 3011Magnesium2 Publications
    Binding sitei301 – 3011Substrate1 Publication
    Active sitei351 – 3511Sequence analysis
    Binding sitei382 – 3821Substrate1 Publication

    GO - Molecular functioni

    • L-fuconate dehydratase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB

    GO - Biological processi

    • carbohydrate catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciXCAM190485:GIXZ-4067-MONOMER.
    SABIO-RKQ8P3K2.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    L-fuconate dehydratase1 Publication (EC:4.2.1.681 Publication1 Publication)
    Short name:
    FucD1 Publication
    Gene namesi
    Ordered Locus Names:XCC4069
    OrganismiXanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
    Taxonomic identifieri190485 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
    Proteomesi
    • UP000001010 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi220 – 2201K → A: Inactive. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 441441L-fuconate dehydratasePRO_0000418813Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi190485.XCC4069.

    Structurei

    Secondary structure

    1
    441
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 1311Combined sources
    Helixi16 – 183Combined sources
    Turni19 – 224Combined sources
    Beta strandi33 – 4311Combined sources
    Beta strandi48 – 558Combined sources
    Helixi60 – 689Combined sources
    Helixi71 – 744Combined sources
    Helixi79 – 846Combined sources
    Helixi86 – 949Combined sources
    Helixi97 – 1015Combined sources
    Beta strandi104 – 1063Combined sources
    Helixi107 – 12721Combined sources
    Helixi132 – 1376Combined sources
    Helixi141 – 1477Combined sources
    Turni154 – 1563Combined sources
    Helixi159 – 16911Combined sources
    Helixi170 – 1723Combined sources
    Helixi173 – 18311Combined sources
    Beta strandi185 – 1939Combined sources
    Helixi199 – 21113Combined sources
    Beta strandi215 – 2206Combined sources
    Helixi225 – 23915Combined sources
    Beta strandi241 – 2488Combined sources
    Helixi255 – 2639Combined sources
    Helixi266 – 2683Combined sources
    Beta strandi270 – 2745Combined sources
    Helixi282 – 29211Combined sources
    Beta strandi297 – 2993Combined sources
    Helixi306 – 31510Combined sources
    Beta strandi319 – 3213Combined sources
    Turni325 – 3273Combined sources
    Helixi330 – 34314Combined sources
    Turni354 – 3563Combined sources
    Helixi357 – 37115Combined sources
    Beta strandi381 – 3833Combined sources
    Helixi388 – 3903Combined sources
    Beta strandi391 – 3933Combined sources
    Beta strandi397 – 4026Combined sources
    Beta strandi407 – 4093Combined sources
    Helixi416 – 4227Combined sources
    Turni424 – 4263Combined sources
    Helixi428 – 4347Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1YEYX-ray2.34A/B/C/D1-441[»]
    2HNEX-ray2.00A/B/C/D1-436[»]
    2HXTX-ray1.70A1-441[»]
    2HXUX-ray1.80A1-441[»]
    ProteinModelPortaliQ8P3K2.
    SMRiQ8P3K2. Positions 1-435.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8P3K2.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni22 – 243Substrate binding1 Publication
    Regioni351 – 3533Substrate binding1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DIA. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113757.
    KOiK18334.
    OMAiSAAYCIL.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 2 hits.
    PfamiPF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q8P3K2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRTIIALETH DVRFPTSREL DGSDAMNPDP DYSAAYVVLR TDGAEDLAGY
    60 70 80 90 100
    GLVFTIGRGN DVQTAAVAAL AEHVVGLSVD KVIADLGAFA RRLTNDSQLR
    110 120 130 140 150
    WLGPEKGVMH MAIGAVINAA WDLAARAANK PLWRFIAELT PEQLVDTIDF
    160 170 180 190 200
    RYLSDALTRD EALAILRDAQ PQRAARTATL IEQGYPAYTT SPGWLGYSDE
    210 220 230 240 250
    KLVRLAKEAV ADGFRTIKLK VGANVQDDIR RCRLARAAIG PDIAMAVDAN
    260 270 280 290 300
    QRWDVGPAID WMRQLAEFDI AWIEEPTSPD DVLGHAAIRQ GITPVPVSTG
    310 320 330 340 350
    EHTQNRVVFK QLLQAGAVDL IQIDAARVGG VNENLAILLL AAKFGVRVFP
    360 370 380 390 400
    HAGGVGLCEL VQHLAMADFV AITGKMEDRA IEFVDHLHQH FLDPVRIQHG
    410 420 430 440
    RYLAPEVPGF SAEMHPASIA EFSYPDGRFW VEDLAASKAK A
    Length:441
    Mass (Da):48,124
    Last modified:October 1, 2002 - v1
    Checksum:i4BAF5BEC1D1E3327
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE008922 Genomic DNA. Translation: AAM43290.1.
    RefSeqiNP_639408.1. NC_003902.1.
    WP_011039138.1. NC_003902.1.

    Genome annotation databases

    EnsemblBacteriaiAAM43290; AAM43290; XCC4069.
    GeneIDi1000844.
    KEGGixcc:XCC4069.
    PATRICi24079370. VBIXanCam115730_4361.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE008922 Genomic DNA. Translation: AAM43290.1.
    RefSeqiNP_639408.1. NC_003902.1.
    WP_011039138.1. NC_003902.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1YEYX-ray2.34A/B/C/D1-441[»]
    2HNEX-ray2.00A/B/C/D1-436[»]
    2HXTX-ray1.70A1-441[»]
    2HXUX-ray1.80A1-441[»]
    ProteinModelPortaliQ8P3K2.
    SMRiQ8P3K2. Positions 1-435.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi190485.XCC4069.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAM43290; AAM43290; XCC4069.
    GeneIDi1000844.
    KEGGixcc:XCC4069.
    PATRICi24079370. VBIXanCam115730_4361.

    Phylogenomic databases

    eggNOGiENOG4105DIA. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113757.
    KOiK18334.
    OMAiSAAYCIL.

    Enzyme and pathway databases

    BioCyciXCAM190485:GIXZ-4067-MONOMER.
    SABIO-RKQ8P3K2.

    Miscellaneous databases

    EvolutionaryTraceiQ8P3K2.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 2 hits.
    PfamiPF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiFUCD_XANCP
    AccessioniPrimary (citable) accession number: Q8P3K2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 5, 2012
    Last sequence update: October 1, 2002
    Last modified: September 7, 2016
    This is version 84 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.