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A4XF23

- MAND_NOVAD

UniProt

A4XF23 - MAND_NOVAD

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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

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
    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: 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

    Protein-protein interaction databases

    STRINGi279238.Saro_3675.

    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:
    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_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:
    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_dom.
    IPR001354. MR/MLE/MAL.
    [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

    « 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: October 29, 2014
    This is version 50 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