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Protein

D-galactonate dehydratase family member Dd703_0947

Gene

Dd703_0947

Organism
Dickeya dadantii (strain Ech703)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Has low dehydratase activity with D-mannonate and D-gluconate, suggesting that these are not physiological substrates and that it has no significant role in the in vivo degradation of these compounds. Has no detectable activity with a panel of 70 other acid sugars (in vitro).1 Publication

Catalytic activityi

D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O.1 Publication
D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O.1 Publication

Cofactori

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

Kineticsi

kcat is 0.04 sec(-1) with D-mannonate. kcat is 0.03 sec(-1) with D-gluconate.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei127 – 1271SubstrateBy similarity
    Active sitei158 – 1581Proton donor/acceptorBy similarity
    Metal bindingi223 – 2231Magnesium1 Publication
    Active sitei225 – 2251Proton donor/acceptorBy similarity
    Metal bindingi249 – 2491Magnesium1 Publication
    Metal bindingi275 – 2751Magnesium1 Publication
    Binding sitei275 – 2751SubstrateBy similarity
    Binding sitei296 – 2961SubstrateBy similarity
    Binding sitei325 – 3251SubstrateBy similarity
    Sitei327 – 3271Important for activity and substrate specificity; Pro is observed in family members with low D-mannonate dehydratase activityBy similarity
    Binding sitei329 – 3291SubstrateBy similarity
    Binding sitei352 – 3521SubstrateBy similarity

    GO - Molecular functioni

    1. gluconate dehydratase activity Source: UniProtKB
    2. magnesium ion binding Source: UniProtKB
    3. mannonate dehydratase activity Source: UniProtKB

    GO - Biological processi

    1. carbohydrate catabolic process Source: UniProtKB
    2. cellular amino acid catabolic process Source: InterPro
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciDDAD579405:GHJU-966-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-galactonate dehydratase family member Dd703_0947 (EC:4.2.1.-)
    Alternative name(s):
    D-gluconate dehydratase (EC:4.2.1.39)
    D-mannonate dehydratase (EC:4.2.1.8)
    Gene namesi
    Ordered Locus Names:Dd703_0947
    OrganismiDickeya dadantii (strain Ech703)
    Taxonomic identifieri579405 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeDickeya
    ProteomesiUP000002734 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 417417D-galactonate dehydratase family member Dd703_0947PRO_0000429883Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi579405.Dd703_0947.

    Structurei

    Secondary structure

    1
    417
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 149Combined sources
    Beta strandi21 – 3010Combined sources
    Beta strandi34 – 385Combined sources
    Helixi42 – 443Combined sources
    Helixi45 – 5410Combined sources
    Helixi56 – 605Combined sources
    Helixi68 – 769Combined sources
    Turni77 – 793Combined sources
    Helixi85 – 10622Combined sources
    Helixi110 – 1134Combined sources
    Beta strandi118 – 13215Combined sources
    Helixi133 – 14513Combined sources
    Beta strandi150 – 1578Combined sources
    Beta strandi190 – 1934Combined sources
    Helixi196 – 21419Combined sources
    Beta strandi216 – 2238Combined sources
    Helixi230 – 24011Combined sources
    Helixi241 – 2433Combined sources
    Beta strandi246 – 2494Combined sources
    Helixi254 – 2596Combined sources
    Helixi260 – 2667Combined sources
    Beta strandi271 – 2733Combined sources
    Helixi280 – 2889Combined sources
    Beta strandi293 – 2953Combined sources
    Helixi299 – 3024Combined sources
    Helixi305 – 31713Combined sources
    Beta strandi328 – 3303Combined sources
    Helixi332 – 34413Combined sources
    Helixi358 – 3636Combined sources
    Beta strandi369 – 3713Combined sources
    Beta strandi374 – 3763Combined sources
    Helixi389 – 3924Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IHCX-ray2.00A/B/C/D/E/F/G/H1-417[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000113758.
    KOiK08323.
    OMAiCHVSTIG.
    OrthoDBiEOG6SBSZM.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N_like.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 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.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    PS00909. MR_MLE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    C6CBG9-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKLKITNVK TILTAPGGID LAVVKVETNE PGLYGLGCAT FTQRIFAVKS
    60 70 80 90 100
    AIDEYMAPFL IGKDPTRIED IWQSAAVSGY WRNGPIMNNA LSGVDMALWD
    110 120 130 140 150
    IKGKLAGMPV YELLGGKCRD GIPLYCHTDG GDEVEVEDNI RARMEEGYQY
    160 170 180 190 200
    VRCQMGMYGG AGTDDLKLIA TQLARAKNIQ PKRSPRSKTP GIYFDPEAYA
    210 220 230 240 250
    KSVPRLFEHL RNKLGFGIEF IHDVHERVTP VTAIQLAKTL EPYQLFYLED
    260 270 280 290 300
    PVAPENIDWL RMLRQQSSTP ISMGELFVNI NEWKPLIDNK LIDYIRCHVS
    310 320 330 340 350
    TIGGITPAKK LAVYSELNGV RTAWHGPGDI SPVGVCANMH LDMSSPNFGI
    360 370 380 390 400
    QEYTPMNDAL REVFPGCPEI DQGYAYVNDK PGLGIDINET LAEKYPCDGG
    410
    IPSWTMARTP DGTASRP
    Length:417
    Mass (Da):46,153
    Last modified:September 1, 2009 - v1
    Checksum:i4FF2BB5D58CFEB69
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP001654 Genomic DNA. Translation: ACS84754.1.
    RefSeqiYP_002986576.1. NC_012880.1.

    Genome annotation databases

    EnsemblBacteriaiACS84754; ACS84754; Dd703_0947.
    KEGGidda:Dd703_0947.
    PATRICi21789142. VBIDicDad95084_1016.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP001654 Genomic DNA. Translation: ACS84754.1.
    RefSeqiYP_002986576.1. NC_012880.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IHCX-ray2.00A/B/C/D/E/F/G/H1-417[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi579405.Dd703_0947.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiACS84754; ACS84754; Dd703_0947.
    KEGGidda:Dd703_0947.
    PATRICi21789142. VBIDicDad95084_1016.

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000113758.
    KOiK08323.
    OMAiCHVSTIG.
    OrthoDBiEOG6SBSZM.

    Enzyme and pathway databases

    BioCyciDDAD579405:GHJU-966-MONOMER.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N_like.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 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.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    PS00909. MR_MLE_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Ech703.
    2. "Discovery of function in the enolase superfamily: D-mannonate and D-gluconate dehydratases in the D-mannonate dehydratase subgroup."
      Wichelecki D.J., Balthazor B.M., Chau A.C., Vetting M.W., Fedorov A.A., Fedorov E.V., Lukk T., Patskovsky Y.V., Stead M.B., Hillerich B.S., Seidel R.D., Almo S.C., Gerlt J.A.
      Biochemistry 53:2722-2731(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiDMGD_DICDC
    AccessioniPrimary (citable) accession number: C6CBG9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 9, 2014
    Last sequence update: September 1, 2009
    Last modified: April 1, 2015
    This is version 36 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

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.