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A4XF23

- MAND_NOVAD

UniProt

A4XF23 - MAND_NOVAD

Protein

D-mannonate dehydratase

Gene

manD

Organism
Novosphingobium aromaticivorans (strain DSM 12444 / F199)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 49 (01 Oct 2014)
      Sequence version 1 (29 May 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).2 Publications

    Catalytic activityi

    D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O.2 Publications

    Cofactori

    Binds 1 Mg2+ ion per subunit.2 Publications

    Kineticsi

    kcat is 1.3 sec(-1) with D-mannonate.2 Publications

      Pathwayi

      Sites

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Binding sitei37 – 371Substrate
      Binding sitei122 – 1221Substrate
      Active sitei159 – 1591Proton donor/acceptor1 Publication
      Metal bindingi210 – 2101Magnesium1 Publication
      Active sitei212 – 2121Proton donor/acceptor1 Publication
      Metal bindingi236 – 2361Magnesium1 Publication
      Metal bindingi262 – 2621Magnesium1 Publication
      Binding sitei262 – 2621Substrate
      Binding sitei283 – 2831Substrate
      Binding sitei312 – 3121Substrate
      Sitei314 – 3141Important for activity and substrate specificity; Ala is observed in family members with high D-mannonate dehydratase activity that have no activity with D-gluconate
      Binding sitei316 – 3161Substrate
      Binding sitei339 – 3391Substrate

      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 - Biological processi

      Carbohydrate metabolism

      Keywords - Ligandi

      Magnesium, Metal-binding

      Enzyme and pathway databases

      BioCyciNARO279238:GHBU-3686-MONOMER.
      UniPathwayiUPA00246.

      Names & Taxonomyi

      Protein namesi
      Recommended name:
      D-mannonate dehydratase (EC:4.2.1.8)
      Short name:
      ManD
      Alternative name(s):
      RspA homolog
      Gene namesi
      Name:manD
      Ordered Locus Names:Saro_3675
      Encoded oniPlasmid pNL21 Publication
      OrganismiNovosphingobium aromaticivorans (strain DSM 12444 / F199)
      Taxonomic identifieri279238 [NCBI]
      Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeNovosphingobium
      ProteomesiUP000009134: Plasmid pNL2

      Pathology & Biotechi

      Mutagenesis

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Mutagenesisi147 – 1471R → A: Abolishes catalytic activity. 1 Publication
      Mutagenesisi147 – 1471R → K: Decreases catalytic activity. 1 Publication
      Mutagenesisi159 – 1591Y → F: Abolishes catalytic activity. 1 Publication
      Mutagenesisi161 – 1699VGRGKLYYE → AGAGGAGAG: Abolishes catalytic activity.
      Mutagenesisi212 – 2121H → N: Abolishes catalytic activity. 1 Publication
      Mutagenesisi271 – 2711K → E: No effect on catalytic activity. 1 Publication
      Mutagenesisi283 – 2831R → A: Abolishes catalytic activity. 1 Publication
      Mutagenesisi312 – 3121H → N: Abolishes catalytic activity. 1 Publication
      Mutagenesisi314 – 3141A → P: Decreases catalytic activity. 1 Publication
      Mutagenesisi339 – 3391E → Q: Abolishes catalytic activity. 1 Publication

      PTM / Processingi

      Molecule processing

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Chaini1 – 402402D-mannonate dehydratasePRO_0000429873Add
      BLAST

      Interactioni

      Subunit structurei

      Homotetramer.1 Publication

      Protein-protein interaction databases

      STRINGi279238.Saro_3675.

      Structurei

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      Links Updated
      EntryMethodResolution (Å)ChainPositionsPDBsum
      2QJJX-ray1.80A/B/C/D1-402[»]
      2QJMX-ray2.20A/B/C/D1-402[»]
      2QJNX-ray2.00A/B/C/D1-402[»]
      4K1WX-ray1.65A/B/C/D1-402[»]
      4K8GX-ray1.25A1-402[»]
      ProteinModelPortaliA4XF23.
      ModBaseiSearch...
      MobiDBiSearch...

      Miscellaneous databases

      EvolutionaryTraceiA4XF23.

      Family & Domainsi

      Sequence similaritiesi

      Phylogenomic databases

      eggNOGiCOG4948.
      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.
      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.
      [Graphical view]

      Sequencei

      Sequence statusi: Complete.

      A4XF23-1 [UniParc]FASTAAdd to Basket

      « Hide

      MKITAARVII TCPGRNFVTL KIETDQGVYG IGDATLNGRE LSVVAYLQEH    50
      VAPCLIGMDP RRIEDIWQYV YRGAYWRRGP VTMRAIAAVD MALWDIKAKM 100
      AGMPLYQLLG GRSRDGIMVY GHANGSDIAE TVEAVGHYID MGYKAIRAQT 150
      GVPGIKDAYG VGRGKLYYEP ADASLPSVTG WDTRKALNYV PKLFEELRKT 200
      YGFDHHLLHD GHHRYTPQEA ANLGKMLEPY QLFWLEDCTP AENQEAFRLV 250
      RQHTVTPLAV GEIFNTIWDA KDLIQNQLID YIRATVVGAG GLTHLRRIAD 300
      LASLYQVRTG CHGATDLSPV TMGCALHFDT WVPNFGIQEY MRHTEETDAV 350
      FPHDYWFEKG ELFVGETPGH GVDIDEELAA KYPYKPAYLP VARLEDGTMW 400
      NW 402
      Length:402
      Mass (Da):45,244
      Last modified:May 29, 2007 - v1
      Checksum:iE22007CDD0538750
      GO

      Sequence databases

      Select the link destinations:
      EMBL
      GenBank
      DDBJ
      Links Updated
      CP000677 Genomic DNA. Translation: ABP64534.1.
      RefSeqiYP_001166060.1. NC_009427.1.

      Genome annotation databases

      EnsemblBacteriaiABP64534; ABP64534; Saro_3675.
      GeneIDi5077823.
      KEGGinar:Saro_3675.
      PATRICi22790486. VBINovAro50627_3893.

      Cross-referencesi

      Sequence databases

      Select the link destinations:
      EMBL
      GenBank
      DDBJ
      Links Updated
      CP000677 Genomic DNA. Translation: ABP64534.1 .
      RefSeqi YP_001166060.1. NC_009427.1.

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      Links Updated
      Entry Method Resolution (Å) Chain Positions PDBsum
      2QJJ X-ray 1.80 A/B/C/D 1-402 [» ]
      2QJM X-ray 2.20 A/B/C/D 1-402 [» ]
      2QJN X-ray 2.00 A/B/C/D 1-402 [» ]
      4K1W X-ray 1.65 A/B/C/D 1-402 [» ]
      4K8G X-ray 1.25 A 1-402 [» ]
      ProteinModelPortali A4XF23.
      ModBasei Search...
      MobiDBi Search...

      Protein-protein interaction databases

      STRINGi 279238.Saro_3675.

      Protocols and materials databases

      Structural Biology Knowledgebase Search...

      Genome annotation databases

      EnsemblBacteriai ABP64534 ; ABP64534 ; Saro_3675 .
      GeneIDi 5077823.
      KEGGi nar:Saro_3675.
      PATRICi 22790486. VBINovAro50627_3893.

      Phylogenomic databases

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

      Enzyme and pathway databases

      UniPathwayi UPA00246 .
      BioCyci NARO279238:GHBU-3686-MONOMER.

      Miscellaneous databases

      EvolutionaryTracei A4XF23.

      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.
      [Graphical view ]
      ProtoNeti Search...

      Publicationsi

      1. "Complete sequence of plasmid pNL2 of Novosphingobium aromaticivorans DSM 12444."
        US DOE Joint Genome Institute
        Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chertkov O., Han C., Thomson S., Schmutz J., Larimer F., Land M., Kyrpides N.
        , Ivanova N., Fredrickson J., Romine M.F., Richardson P.
        Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases
        Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
        Strain: DSM 12444 / F199.
        Plasmid: pNL2
      2. "Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans."
        Rakus J.F., Fedorov A.A., Fedorov E.V., Glasner M.E., Vick J.E., Babbitt P.C., Almo S.C., Gerlt J.A.
        Biochemistry 46:12896-12908(2007) [PubMed] [Europe PMC] [Abstract]
        Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH D-MANNONIC ACID AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT, ACTIVE SITE, MUTAGENESIS OF ARG-147; TYR-159; HIS-212; LYS-271; ARG-283; HIS-312 AND GLU-339.
        Strain: DSM 12444 / F199.
      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 (1.25 ANGSTROMS) IN COMPLEX D-MANNONIC ACID AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF 161-VAL--GLU-169 AND ALA-314.
        Strain: DSM 12444 / F199.

      Entry informationi

      Entry nameiMAND_NOVAD
      AccessioniPrimary (citable) accession number: A4XF23
      Entry historyi
      Integrated into UniProtKB/Swiss-Prot: July 9, 2014
      Last sequence update: May 29, 2007
      Last modified: October 1, 2014
      This is version 49 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, Plasmid, Reference proteome

      Documents

      1. PATHWAY comments
        Index of metabolic and biosynthesis pathways
      2. PDB cross-references
        Index of Protein Data Bank (PDB) cross-references
      3. SIMILARITY comments
        Index of protein domains and families

      External Data

      Dasty 3