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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

Manual assertion based on experiment ini

      Sites

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Binding sitei127SubstrateBy similarity1
      Active sitei158Proton donor/acceptorBy similarity1
      Metal bindingi223Magnesium1 Publication1
      Active sitei225Proton donor/acceptorBy similarity1
      Metal bindingi249Magnesium1 Publication1
      Metal bindingi275Magnesium1 Publication1
      Binding sitei275SubstrateBy similarity1
      Binding sitei296SubstrateBy similarity1
      Binding sitei325SubstrateBy similarity1
      Sitei327Important for activity and substrate specificity; Pro is observed in family members with low D-mannonate dehydratase activityBy similarity1
      Binding sitei329SubstrateBy similarity1
      Binding sitei352SubstrateBy similarity1

      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-956-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesPectobacteriaceaeDickeya
      Proteomesi
      • UP000002734 Componenti: Chromosome

      PTM / Processingi

      Molecule processing

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      ChainiPRO_00004298831 – 417D-galactonate dehydratase family member Dd703_0947Add BLAST417

      Interactioni

      Protein-protein interaction databases

      STRINGi579405.Dd703_0947.

      Structurei

      Secondary structure

      1417
      Legend: HelixTurnBeta strandPDB Structure known for this area
      Show more details
      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Beta strandi6 – 14Combined sources9
      Beta strandi21 – 30Combined sources10
      Beta strandi34 – 38Combined sources5
      Helixi42 – 44Combined sources3
      Helixi45 – 54Combined sources10
      Helixi56 – 60Combined sources5
      Helixi68 – 76Combined sources9
      Turni77 – 79Combined sources3
      Helixi85 – 106Combined sources22
      Helixi110 – 113Combined sources4
      Beta strandi118 – 132Combined sources15
      Helixi133 – 145Combined sources13
      Beta strandi150 – 157Combined sources8
      Beta strandi190 – 193Combined sources4
      Helixi196 – 214Combined sources19
      Beta strandi216 – 223Combined sources8
      Helixi230 – 240Combined sources11
      Helixi241 – 243Combined sources3
      Beta strandi246 – 249Combined sources4
      Helixi254 – 259Combined sources6
      Helixi260 – 266Combined sources7
      Beta strandi271 – 273Combined sources3
      Helixi280 – 288Combined sources9
      Beta strandi293 – 295Combined sources3
      Helixi299 – 302Combined sources4
      Helixi305 – 317Combined sources13
      Beta strandi328 – 330Combined sources3
      Helixi332 – 344Combined sources13
      Helixi358 – 363Combined sources6
      Beta strandi369 – 371Combined sources3
      Beta strandi374 – 376Combined sources3
      Helixi389 – 392Combined sources4

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      4IHCX-ray2.00A/B/C/D/E/F/G/H1-417[»]
      ProteinModelPortaliC6CBG9.
      SMRiC6CBG9.
      ModBaseiSearch...
      MobiDBiSearch...

      Family & Domainsi

      Sequence similaritiesi

      Phylogenomic databases

      eggNOGiENOG4105CXK. Bacteria.
      COG4948. LUCA.
      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiFVNINEW.
      OrthoDBiPOG091H0FES.

      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. 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.
      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.

      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.

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      4IHCX-ray2.00A/B/C/D/E/F/G/H1-417[»]
      ProteinModelPortaliC6CBG9.
      SMRiC6CBG9.
      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

      eggNOGiENOG4105CXK. Bacteria.
      COG4948. LUCA.
      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiFVNINEW.
      OrthoDBiPOG091H0FES.

      Enzyme and pathway databases

      BioCyciDDAD579405:GHJU-956-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. 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.
      PROSITEiPS00908. MR_MLE_1. 1 hit.
      PS00909. MR_MLE_2. 1 hit.
      [Graphical view]
      ProtoNetiSearch...

      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: November 2, 2016
      This is version 43 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

      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.