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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

      Sites

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Binding sitei37 – 371Substrate
      Binding sitei122 – 1221SubstrateBy similarity
      Active sitei159 – 1591Proton donor/acceptorBy similarity
      Metal bindingi211 – 2111Magnesium1 Publication
      Active sitei213 – 2131Proton donor/acceptorBy similarity
      Metal bindingi237 – 2371Magnesium1 Publication
      Metal bindingi263 – 2631Magnesium1 Publication
      Binding sitei263 – 2631Substrate
      Binding sitei284 – 2841Substrate
      Binding sitei313 – 3131Substrate
      Sitei315 – 3151Important for activity and substrate specificity; Pro is observed in family members with low D-mannonate dehydratase activity
      Binding sitei317 – 3171Substrate
      Binding sitei340 – 3401Substrate

      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)LengthDescriptionGraphical viewFeature identifierActions
      Mutagenesisi163 – 1708KTPGERYE → GAGGAGAG: Abolishes catalytic activity.
      Mutagenesisi313 – 3131H → N: Abolishes activity with D-gluconate and D-mannonate. 1 Publication
      Mutagenesisi313 – 3131H → Q: Abolishes activity with D-gluconate. No effect on activity with D-mannonate. 1 Publication
      Mutagenesisi315 – 3151P → A: Strongly increases activity with D-mannonate. Slightly decreases activity with D-gluconate. 1 Publication

      PTM / Processingi

      Molecule processing

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Chaini1 – 403403D-galactonate dehydratase family member ManDPRO_0000429881Add
      BLAST

      Interactioni

      Protein-protein interaction databases

      STRINGi290398.Csal_2974.

      Structurei

      Secondary structure

      1
      403
      Legend: HelixTurnBeta strand
      Show more details
      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Beta strandi2 – 1110Combined sources
      Beta strandi13 – 153Combined sources
      Beta strandi17 – 248Combined sources
      Beta strandi29 – 335Combined sources
      Helixi40 – 5011Combined sources
      Helixi52 – 554Combined sources
      Helixi63 – 7311Combined sources
      Turni74 – 763Combined sources
      Helixi80 – 10122Combined sources
      Helixi105 – 1084Combined sources
      Beta strandi115 – 12713Combined sources
      Helixi128 – 14013Combined sources
      Beta strandi144 – 1507Combined sources
      Beta strandi174 – 1763Combined sources
      Beta strandi179 – 1824Combined sources
      Helixi184 – 20219Combined sources
      Beta strandi204 – 2118Combined sources
      Helixi218 – 22811Combined sources
      Helixi229 – 2313Combined sources
      Beta strandi234 – 2374Combined sources
      Helixi245 – 2484Combined sources
      Helixi249 – 2546Combined sources
      Beta strandi259 – 2613Combined sources
      Helixi268 – 2703Combined sources
      Helixi272 – 2765Combined sources
      Beta strandi281 – 2833Combined sources
      Turni287 – 2915Combined sources
      Helixi292 – 30413Combined sources
      Turni305 – 3073Combined sources
      Beta strandi309 – 3124Combined sources
      Helixi320 – 33213Combined sources
      Beta strandi336 – 3405Combined sources
      Helixi346 – 3516Combined sources
      Beta strandi357 – 3593Combined sources
      Beta strandi362 – 3643Combined sources
      Beta strandi368 – 3736Combined sources
      Helixi377 – 3804Combined sources
      Beta strandi392 – 3954Combined sources

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      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. Positions 1-386.
      ModBaseiSearch...
      MobiDBiSearch...

      Miscellaneous databases

      EvolutionaryTraceiQ1QT89.

      Family & Domainsi

      Sequence similaritiesi

      Phylogenomic databases

      eggNOGiENOG4105CXK. Bacteria.
      COG4948. LUCA.
      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiNQRAFEI.
      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. 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
      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. Positions 1-386.
      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.
      OrthoDBiEOG6SBSZM.

      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...

      Publicationsi

      « Hide 'large scale' publications
      1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
        Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768.
      2. "Crystal structure of the mutant P317A of D-mannonate dehydratase from Chromohalobacter salexigens complexed with Mg and D-Gluconate."
        Fedorov A.A., Fedorov E.V., Wichelecki D., Gerlt J.A., Almo S.C.
        Submitted (FEB-2011) to the PDB data bank
        Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 2-403 IN COMPLEX WITH MAGNESIUM.
      3. "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 (1.45 ANGSTROMS) OF 2-403 IN COMPLEXES WITH MAGNESIUM; D-MANNONATE AND 2-KETO-3-DEOXY-D-GLUCONATE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF HIS-313 AND PRO-315.
        Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768.

      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: January 20, 2016
      This is version 72 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.