Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

D-mannonate dehydratase

Gene

manD

Organism
Novosphingobium aromaticivorans (strain DSM 12444 / F199)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Mg2+2 PublicationsNote: Binds 1 Mg2+ ion per subunit.2 Publications

Kineticsi

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

      Pathway: pentose and glucuronate interconversion

      This protein is involved in the pathway pentose and glucuronate interconversion, which is part of Carbohydrate metabolism.
      View all proteins of this organism that are known to be involved in the pathway pentose and glucuronate interconversion and in Carbohydrate metabolism.

      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

      • 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 - 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 Componenti: 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. 1 Publication
      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

      Structurei

      Secondary structure

      1
      402
      Legend: HelixTurnBeta strand
      Show more details
      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Beta strandi3 – 119Combined sources
      Beta strandi13 – 153Combined sources
      Beta strandi17 – 2711Combined sources
      Beta strandi29 – 335Combined sources
      Helixi40 – 4910Combined sources
      Helixi51 – 555Combined sources
      Helixi63 – 7311Combined sources
      Helixi80 – 10122Combined sources
      Helixi105 – 1095Combined sources
      Beta strandi115 – 12713Combined sources
      Helixi128 – 14013Combined sources
      Beta strandi144 – 1507Combined sources
      Beta strandi173 – 1753Combined sources
      Beta strandi178 – 1814Combined sources
      Helixi183 – 1875Combined sources
      Helixi190 – 20112Combined sources
      Beta strandi203 – 2108Combined sources
      Helixi217 – 22711Combined sources
      Helixi228 – 2303Combined sources
      Beta strandi233 – 2375Combined sources
      Helixi244 – 2474Combined sources
      Helixi248 – 2536Combined sources
      Beta strandi258 – 2603Combined sources
      Helixi267 – 2693Combined sources
      Helixi271 – 2755Combined sources
      Beta strandi280 – 2823Combined sources
      Turni286 – 2905Combined sources
      Helixi291 – 30414Combined sources
      Beta strandi308 – 3114Combined sources
      Helixi319 – 33113Combined sources
      Beta strandi335 – 3395Combined sources
      Helixi345 – 3506Combined sources
      Beta strandi353 – 3586Combined sources
      Beta strandi361 – 3644Combined sources
      Beta strandi368 – 3725Combined sources
      Helixi376 – 3794Combined sources
      Beta strandi391 – 3944Combined sources

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      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.
      OMAiRAQSGVP.
      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. 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

              10         20         30         40         50
      MKITAARVII TCPGRNFVTL KIETDQGVYG IGDATLNGRE LSVVAYLQEH
      60 70 80 90 100
      VAPCLIGMDP RRIEDIWQYV YRGAYWRRGP VTMRAIAAVD MALWDIKAKM
      110 120 130 140 150
      AGMPLYQLLG GRSRDGIMVY GHANGSDIAE TVEAVGHYID MGYKAIRAQT
      160 170 180 190 200
      GVPGIKDAYG VGRGKLYYEP ADASLPSVTG WDTRKALNYV PKLFEELRKT
      210 220 230 240 250
      YGFDHHLLHD GHHRYTPQEA ANLGKMLEPY QLFWLEDCTP AENQEAFRLV
      260 270 280 290 300
      RQHTVTPLAV GEIFNTIWDA KDLIQNQLID YIRATVVGAG GLTHLRRIAD
      310 320 330 340 350
      LASLYQVRTG CHGATDLSPV TMGCALHFDT WVPNFGIQEY MRHTEETDAV
      360 370 380 390 400
      FPHDYWFEKG ELFVGETPGH GVDIDEELAA KYPYKPAYLP VARLEDGTMW

      NW
      Length:402
      Mass (Da):45,244
      Last modified:May 29, 2007 - v1
      Checksum:iE22007CDD0538750
      GO

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      CP000677 Genomic DNA. Translation: ABP64534.1.
      RefSeqiWP_011906920.1. NC_009427.1.
      YP_001166060.1. NC_009427.1.

      Genome annotation databases

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

      Cross-referencesi

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      CP000677 Genomic DNA. Translation: ABP64534.1.
      RefSeqiWP_011906920.1. NC_009427.1.
      YP_001166060.1. NC_009427.1.

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      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...

      Protocols and materials databases

      Structural Biology KnowledgebaseSearch...

      Genome annotation databases

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

      Phylogenomic databases

      eggNOGiCOG4948.
      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiRAQSGVP.
      OrthoDBiEOG6SBSZM.

      Enzyme and pathway databases

      UniPathwayiUPA00246.
      BioCyciNARO279238:GHBU-3686-MONOMER.

      Miscellaneous databases

      EvolutionaryTraceiA4XF23.

      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. 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]
      ProtoNetiSearch...

      Publicationsi

      « Hide 'large scale' publications
      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: June 24, 2015
      This is version 56 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

      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 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.