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Protein

D-galactonate dehydratase family member ManD

Gene

manD

Organism
Chromohalobacter salexigens (strain DSM 3043 / ATCC BAA-138 / NCIMB 13768)
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 0.02 sec(-1) with D-mannonate. kcat is 0.04 sec(-1) with D-gluconate.1 Publication

Manual assertion based on experiment ini

      Sites

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Binding sitei37Substrate1
      Binding sitei122SubstrateBy similarity1
      Active sitei159Proton donor/acceptorBy similarity1
      Metal bindingi211Magnesium1 Publication1
      Active sitei213Proton donor/acceptorBy similarity1
      Metal bindingi237Magnesium1 Publication1
      Metal bindingi263Magnesium1 Publication1
      Binding sitei263Substrate1
      Binding sitei284Substrate1
      Binding sitei313Substrate1
      Sitei315Important for activity and substrate specificity; Pro is observed in family members with low D-mannonate dehydratase activity1
      Binding sitei317Substrate1
      Binding sitei340Substrate1

      GO - Molecular functioni

      • gluconate dehydratase activity Source: UniProtKB-EC
      • 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

      Names & Taxonomyi

      Protein namesi
      Recommended name:
      D-galactonate dehydratase family member ManD (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
      Name:manD
      Ordered Locus Names:Csal_2974
      OrganismiChromohalobacter salexigens (strain DSM 3043 / ATCC BAA-138 / NCIMB 13768)
      Taxonomic identifieri290398 [NCBI]
      Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaOceanospirillalesHalomonadaceaeChromohalobacter
      Proteomesi
      • UP000000239 Componenti: Chromosome

      Pathology & Biotechi

      Mutagenesis

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Mutagenesisi163 – 170KTPGERYE → GAGGAGAG: Abolishes catalytic activity. 8
      Mutagenesisi313H → N: Abolishes activity with D-gluconate and D-mannonate. 1 Publication1
      Mutagenesisi313H → Q: Abolishes activity with D-gluconate. No effect on activity with D-mannonate. 1 Publication1
      Mutagenesisi315P → A: Strongly increases activity with D-mannonate. Slightly decreases activity with D-gluconate. 1 Publication1

      PTM / Processingi

      Molecule processing

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      ChainiPRO_00004298811 – 403D-galactonate dehydratase family member ManDAdd BLAST403

      Interactioni

      Protein-protein interaction databases

      STRINGi290398.Csal_2974.

      Structurei

      Secondary structure

      1403
      Legend: HelixTurnBeta strandPDB Structure known for this area
      Show more details
      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Beta strandi2 – 11Combined sources10
      Beta strandi13 – 15Combined sources3
      Beta strandi17 – 24Combined sources8
      Beta strandi29 – 33Combined sources5
      Helixi40 – 50Combined sources11
      Helixi52 – 55Combined sources4
      Helixi63 – 73Combined sources11
      Turni74 – 76Combined sources3
      Helixi80 – 101Combined sources22
      Helixi105 – 108Combined sources4
      Beta strandi115 – 127Combined sources13
      Helixi128 – 140Combined sources13
      Beta strandi144 – 150Combined sources7
      Beta strandi174 – 176Combined sources3
      Beta strandi179 – 182Combined sources4
      Helixi184 – 202Combined sources19
      Beta strandi204 – 211Combined sources8
      Helixi218 – 228Combined sources11
      Helixi229 – 231Combined sources3
      Beta strandi234 – 237Combined sources4
      Helixi245 – 248Combined sources4
      Helixi249 – 254Combined sources6
      Beta strandi259 – 261Combined sources3
      Helixi268 – 270Combined sources3
      Helixi272 – 276Combined sources5
      Beta strandi281 – 283Combined sources3
      Turni287 – 291Combined sources5
      Helixi292 – 304Combined sources13
      Turni305 – 307Combined sources3
      Beta strandi309 – 312Combined sources4
      Helixi320 – 332Combined sources13
      Beta strandi336 – 340Combined sources5
      Helixi346 – 351Combined sources6
      Beta strandi357 – 359Combined sources3
      Beta strandi362 – 364Combined sources3
      Beta strandi368 – 373Combined sources6
      Helixi377 – 380Combined sources4
      Beta strandi392 – 395Combined sources4

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      3BSMX-ray2.20A/B/C/D2-403[»]
      3OW1X-ray1.80A/B/C/D/E/F/G/H2-403[»]
      3P93X-ray1.80A/B/C/D/E/F/G/H2-403[»]
      3PK7X-ray1.64A/B/C/D/E/F/G/H2-403[»]
      3QKEX-ray1.55A/B/C/D/E/F/G/H2-403[»]
      3RGTX-ray1.90A/B/C/D2-403[»]
      4F4RX-ray1.80A1-403[»]
      4K2SX-ray1.70A/B/C/D/E/F/G/H2-403[»]
      4KPLX-ray2.00A/B/C/D/E/F/G/H1-403[»]
      4KT2X-ray1.80A/B/C/D/E/F/G/H1-403[»]
      4KWSX-ray1.64A/B/C/D/E/F/G/H2-403[»]
      ProteinModelPortaliQ1QT89.
      SMRiQ1QT89.
      ModBaseiSearch...
      MobiDBiSearch...

      Miscellaneous databases

      EvolutionaryTraceiQ1QT89.

      Family & Domainsi

      Sequence similaritiesi

      Phylogenomic databases

      eggNOGiENOG4105CXK. Bacteria.
      COG4948. LUCA.
      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiNQRAFEI.
      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.
      [Graphical view]

      Sequencei

      Sequence statusi: Complete.

      Q1QT89-1 [UniParc]FASTAAdd to basket

      « Hide

              10         20         30         40         50
      MKIRDAYTIV TCPGRNFVTL KIVTESGTHG IGDATLNGRE MAVAAYLDEH
      60 70 80 90 100
      VVPALIGRDA GRIEDTWQYL YRGAYWRRGP VTMTAIAAVD MALWDIKAKA
      110 120 130 140 150
      AGMPLYQLLG GKSRERVMTY AHCTGQTIED CLGEVARHVE LGYRAVRVQS
      160 170 180 190 200
      GVPGIETTYG VAKTPGERYE PADSSLPAEH VWSTEKYLNH APKLFAAVRE
      210 220 230 240 250
      RFGDDLHVLH DVHHRLTPIE AARLGKAVEP YHLFWLEDCV PAENQESLRL
      260 270 280 290 300
      IREHTTTPLA IGEVFNSIHD CRELIQNQWI DYIRMPLTHG GGITAMRRVA
      310 320 330 340 350
      DLASLYHVRT GFHGPTDLSP VCLGAAIHFD TWVPNFGIQE HMPHTDETDA
      360 370 380 390 400
      VFPHDYRFED GHFLAGESPG HGVDIDEELA AKYPYERASL PVNRLEDGTL

      WHW
      Length:403
      Mass (Da):45,207
      Last modified:May 16, 2006 - v1
      Checksum:i21717195BC4284E9
      GO

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      CP000285 Genomic DNA. Translation: ABE60319.1.
      RefSeqiWP_011508265.1. NC_007963.1.

      Genome annotation databases

      EnsemblBacteriaiABE60319; ABE60319; Csal_2974.
      KEGGicsa:Csal_2974.
      PATRICi21449804. VBIChrSal113723_2988.

      Cross-referencesi

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      CP000285 Genomic DNA. Translation: ABE60319.1.
      RefSeqiWP_011508265.1. NC_007963.1.

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      3BSMX-ray2.20A/B/C/D2-403[»]
      3OW1X-ray1.80A/B/C/D/E/F/G/H2-403[»]
      3P93X-ray1.80A/B/C/D/E/F/G/H2-403[»]
      3PK7X-ray1.64A/B/C/D/E/F/G/H2-403[»]
      3QKEX-ray1.55A/B/C/D/E/F/G/H2-403[»]
      3RGTX-ray1.90A/B/C/D2-403[»]
      4F4RX-ray1.80A1-403[»]
      4K2SX-ray1.70A/B/C/D/E/F/G/H2-403[»]
      4KPLX-ray2.00A/B/C/D/E/F/G/H1-403[»]
      4KT2X-ray1.80A/B/C/D/E/F/G/H1-403[»]
      4KWSX-ray1.64A/B/C/D/E/F/G/H2-403[»]
      ProteinModelPortaliQ1QT89.
      SMRiQ1QT89.
      ModBaseiSearch...
      MobiDBiSearch...

      Protein-protein interaction databases

      STRINGi290398.Csal_2974.

      Protocols and materials databases

      Structural Biology KnowledgebaseSearch...

      Genome annotation databases

      EnsemblBacteriaiABE60319; ABE60319; Csal_2974.
      KEGGicsa:Csal_2974.
      PATRICi21449804. VBIChrSal113723_2988.

      Phylogenomic databases

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

      Miscellaneous databases

      EvolutionaryTraceiQ1QT89.

      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.
      [Graphical view]
      ProtoNetiSearch...

      Entry informationi

      Entry nameiDMGD_CHRSD
      AccessioniPrimary (citable) accession number: Q1QT89
      Entry historyi
      Integrated into UniProtKB/Swiss-Prot: July 9, 2014
      Last sequence update: May 16, 2006
      Last modified: November 2, 2016
      This is version 75 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.