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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

      • gluconate dehydratase activity Source: UniProtKB
      • magnesium ion binding Source: UniProtKB
      • mannonate dehydratase activity Source: UniProtKB

      GO - Biological processi

      • carbohydrate catabolic process Source: UniProtKB
      • 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[»]
      ProteinModelPortaliC6CBG9.
      ModBaseiSearch...
      MobiDBiSearch...

      Family & Domainsi

      Sequence similaritiesi

      Phylogenomic databases

      eggNOGiCOG4948.
      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiRCHVSTI.
      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.
      RefSeqiWP_012764572.1. 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.
      RefSeqiWP_012764572.1. 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[»]
      ProteinModelPortaliC6CBG9.
      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.
      OMAiRCHVSTI.
      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(2014) [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: July 22, 2015
      This is version 38 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.