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C6CBG9

- DMGD_DICDC

UniProt

C6CBG9 - DMGD_DICDC

Protein

D-galactonate dehydratase family member Dd703_0947

Gene

Dd703_0947

Organism
Dickeya dadantii (strain Ech703)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 32 (01 Oct 2014)
      Sequence version 1 (01 Sep 2009)
      Previous versions | rss
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    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

    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

      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: 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

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      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.
      OMAiGIQEYTP.
      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.
      IPR001354. MR_MLE.
      [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

      MSKLKITNVK TILTAPGGID LAVVKVETNE PGLYGLGCAT FTQRIFAVKS    50
      AIDEYMAPFL IGKDPTRIED IWQSAAVSGY WRNGPIMNNA LSGVDMALWD 100
      IKGKLAGMPV YELLGGKCRD GIPLYCHTDG GDEVEVEDNI RARMEEGYQY 150
      VRCQMGMYGG AGTDDLKLIA TQLARAKNIQ PKRSPRSKTP GIYFDPEAYA 200
      KSVPRLFEHL RNKLGFGIEF IHDVHERVTP VTAIQLAKTL EPYQLFYLED 250
      PVAPENIDWL RMLRQQSSTP ISMGELFVNI NEWKPLIDNK LIDYIRCHVS 300
      TIGGITPAKK LAVYSELNGV RTAWHGPGDI SPVGVCANMH LDMSSPNFGI 350
      QEYTPMNDAL REVFPGCPEI DQGYAYVNDK PGLGIDINET LAEKYPCDGG 400
      IPSWTMARTP DGTASRP 417
      Length:417
      Mass (Da):46,153
      Last modified:September 1, 2009 - v1
      Checksum:i4FF2BB5D58CFEB69
      GO

      Sequence databases

      Select the link destinations:
      EMBL
      GenBank
      DDBJ
      Links Updated
      CP001654 Genomic DNA. Translation: ACS84754.1.
      RefSeqiYP_002986576.1. NC_012880.1.

      Genome annotation databases

      EnsemblBacteriaiACS84754; ACS84754; Dd703_0947.
      GeneIDi8090089.
      KEGGidda:Dd703_0947.
      PATRICi21789142. VBIDicDad95084_1016.

      Cross-referencesi

      Sequence databases

      Select the link destinations:
      EMBL
      GenBank
      DDBJ
      Links Updated
      CP001654 Genomic DNA. Translation: ACS84754.1 .
      RefSeqi YP_002986576.1. NC_012880.1.

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      Links Updated
      Entry Method Resolution (Å) Chain Positions PDBsum
      4IHC X-ray 2.00 A/B/C/D/E/F/G/H 1-417 [» ]
      ProteinModelPortali C6CBG9.
      ModBasei Search...
      MobiDBi Search...

      Protein-protein interaction databases

      STRINGi 579405.Dd703_0947.

      Protocols and materials databases

      Structural Biology Knowledgebase Search...

      Genome annotation databases

      EnsemblBacteriai ACS84754 ; ACS84754 ; Dd703_0947 .
      GeneIDi 8090089.
      KEGGi dda:Dd703_0947.
      PATRICi 21789142. VBIDicDad95084_1016.

      Phylogenomic databases

      eggNOGi COG4948.
      HOGENOMi HOG000113758.
      KOi K08323.
      OMAi GIQEYTP.
      OrthoDBi EOG6SBSZM.

      Enzyme and pathway databases

      BioCyci DDAD579405:GHJU-966-MONOMER.

      Family and domain databases

      Gene3Di 3.20.20.120. 1 hit.
      3.30.390.10. 1 hit.
      InterProi IPR029065. Enolase_C-like.
      IPR029017. Enolase_N_like.
      IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
      IPR013342. Mandelate_racemase_C.
      IPR013341. Mandelate_racemase_N.
      IPR001354. MR_MLE.
      [Graphical view ]
      PANTHERi PTHR13794. PTHR13794. 1 hit.
      Pfami PF01188. MR_MLE. 1 hit.
      PF02746. MR_MLE_N. 1 hit.
      [Graphical view ]
      SMARTi SM00922. MR_MLE. 1 hit.
      [Graphical view ]
      SUPFAMi SSF51604. SSF51604. 1 hit.
      SSF54826. SSF54826. 1 hit.
      PROSITEi PS00908. MR_MLE_1. 1 hit.
      PS00909. MR_MLE_2. 1 hit.
      [Graphical view ]
      ProtoNeti Search...

      Publicationsi

      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: October 1, 2014
      This is version 32 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