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Protein

D(-)-tartrate dehydratase

Gene

tarD

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of D-tartrate to oxaloacetate.1 Publication

Catalytic activityi

(S,S)-tartrate = oxaloacetate + H2O.1 Publication

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Kineticsi

kcat is 7.3 sec(-1) for D-tartrate.

  1. KM=0.086 mM for D-tartrate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei21 – 211Substrate
    Binding sitei55 – 551Substrate
    Sitei55 – 551Transition state stabilizer
    Binding sitei102 – 1021Substrate
    Binding sitei156 – 1561Substrate
    Binding sitei182 – 1821Substrate
    Sitei182 – 1821Transition state stabilizer
    Active sitei184 – 1841acceptor1 Publication
    Metal bindingi213 – 2131Magnesium1 Publication
    Metal bindingi239 – 2391Magnesium1 Publication
    Binding sitei239 – 2391Substrate
    Metal bindingi265 – 2651Magnesium1 Publication
    Binding sitei265 – 2651Substrate
    Sitei292 – 2921Increases basicity of active site His
    Active sitei322 – 3221Proton donor/acceptor1 Publication
    Binding sitei322 – 3221Substrate
    Sitei341 – 3411Transition state stabilizer

    GO - Molecular functioni

    • D(-)-tartrate dehydratase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB

    GO - Biological processi

    • protein homooligomerization Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciBJAP224911:GJEJ-6781-MONOMER.
    SABIO-RKQ89FH0.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D(-)-tartrate dehydratase (EC:4.2.1.81)
    Gene namesi
    Name:tarD
    Ordered Locus Names:bll6730
    OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
    Taxonomic identifieri224911 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
    ProteomesiUP000002526 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi102 – 1021K → A or M: Loss of dehydration activity. 1 Publication
    Mutagenesisi184 – 1841K → A: Loss of dehydration activity. 1 Publication
    Mutagenesisi184 – 1841K → R: Reduced dehydration activity. 1 Publication
    Mutagenesisi322 – 3221H → N: Decreased but measurable dehydration activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 389389D(-)-tartrate dehydratasePRO_0000430443Add
    BLAST

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.1 Publication

    Protein-protein interaction databases

    STRINGi224911.bll6730.

    Structurei

    Secondary structure

    1
    389
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 1410Combined sources
    Beta strandi30 – 4112Combined sources
    Beta strandi43 – 5210Combined sources
    Helixi61 – 666Combined sources
    Helixi68 – 736Combined sources
    Helixi77 – 793Combined sources
    Beta strandi85 – 884Combined sources
    Helixi90 – 978Combined sources
    Turni98 – 1003Combined sources
    Helixi108 – 12821Combined sources
    Helixi132 – 1398Combined sources
    Beta strandi147 – 1537Combined sources
    Helixi163 – 17412Combined sources
    Turni175 – 1773Combined sources
    Beta strandi179 – 1846Combined sources
    Beta strandi186 – 1883Combined sources
    Helixi190 – 20415Combined sources
    Turni205 – 2073Combined sources
    Beta strandi209 – 2135Combined sources
    Helixi220 – 23011Combined sources
    Beta strandi236 – 2394Combined sources
    Helixi247 – 2537Combined sources
    Turni254 – 2563Combined sources
    Beta strandi261 – 2633Combined sources
    Helixi270 – 27910Combined sources
    Turni284 – 2863Combined sources
    Turni293 – 2975Combined sources
    Helixi299 – 31113Combined sources
    Helixi316 – 3183Combined sources
    Helixi326 – 33510Combined sources
    Beta strandi340 – 3423Combined sources
    Turni348 – 3503Combined sources
    Beta strandi363 – 3653Combined sources
    Helixi374 – 3763Combined sources
    Helixi378 – 3858Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1TZZX-ray1.86A/B1-389[»]
    2DW6X-ray2.30A/B/C/D1-389[»]
    2DW7X-ray2.50A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-389[»]
    ProteinModelPortaliQ89FH0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ89FH0.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni182 – 1843Substrate binding
    Regioni213 – 2153Substrate binding
    Regioni341 – 3433Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    HOGENOMiHOG000257327.
    InParanoidiQ89FH0.
    OrthoDBiEOG6Q2SGK.
    PhylomeDBiQ89FH0.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q89FH0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSVRIVDVRE ITKPISSPIR NAYIDFTKMT TSLVAVVTDV VREGKRVVGY
    60 70 80 90 100
    GFNSNGRYGQ GGLIRERFAS RILEADPKKL LNEAGDNLDP DKVWAAMMIN
    110 120 130 140 150
    EKPGGHGERS VAVGTIDMAV WDAVAKIAGK PLFRLLAERH GVKANPRVFV
    160 170 180 190 200
    YAAGGYYYPG KGLSMLRGEM RGYLDRGYNV VKMKIGGAPI EEDRMRIEAV
    210 220 230 240 250
    LEEIGKDAQL AVDANGRFNL ETGIAYAKML RDYPLFWYEE VGDPLDYALQ
    260 270 280 290 300
    AALAEFYPGP MATGENLFSH QDARNLLRYG GMRPDRDWLQ FDCALSYGLC
    310 320 330 340 350
    EYQRTLEVLK THGWSPSRCI PHGGHQMSLN IAAGLGLGGN ESYPDLFQPY
    360 370 380
    GGFPDGVRVE NGHITMPDLP GIGFEGKSDL YKEMKALAE
    Length:389
    Mass (Da):43,058
    Last modified:June 1, 2003 - v1
    Checksum:i0FE177A59AB2F82C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000040 Genomic DNA. Translation: BAC51995.1.
    RefSeqiNP_773370.1. NC_004463.1.
    WP_011089469.1. NC_004463.1.

    Genome annotation databases

    EnsemblBacteriaiBAC51995; BAC51995; BAC51995.
    GeneIDi1050053.
    KEGGibja:bll6730.
    PATRICi21197324. VBIBraJap65052_6896.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000040 Genomic DNA. Translation: BAC51995.1.
    RefSeqiNP_773370.1. NC_004463.1.
    WP_011089469.1. NC_004463.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1TZZX-ray1.86A/B1-389[»]
    2DW6X-ray2.30A/B/C/D1-389[»]
    2DW7X-ray2.50A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-389[»]
    ProteinModelPortaliQ89FH0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224911.bll6730.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAC51995; BAC51995; BAC51995.
    GeneIDi1050053.
    KEGGibja:bll6730.
    PATRICi21197324. VBIBraJap65052_6896.

    Phylogenomic databases

    HOGENOMiHOG000257327.
    InParanoidiQ89FH0.
    OrthoDBiEOG6Q2SGK.
    PhylomeDBiQ89FH0.

    Enzyme and pathway databases

    BioCyciBJAP224911:GJEJ-6781-MONOMER.
    SABIO-RKQ89FH0.

    Miscellaneous databases

    EvolutionaryTraceiQ89FH0.
    PROiQ89FH0.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.
    2. "Finding Sequences for over 270 Orphan Enzymes."
      Shearer A.G., Altman T., Rhee C.D.
      PLoS ONE 9:E97250-E97250(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION.
    3. "Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum."
      Yew W.S., Fedorov A.A., Fedorov E.V., Wood B.M., Almo S.C., Gerlt J.A.
      Biochemistry 45:14598-14608(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF MUTANT LYS-184 IN COMPLEX WITH D(-)-TARTRATE AND MAGNESIUM, COFACTOR, ACTIVE SITE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, MUTAGENESIS OF LYS-102; LYS-184 AND HIS-322.

    Entry informationi

    Entry nameiTARD_BRADU
    AccessioniPrimary (citable) accession number: Q89FH0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 2014
    Last sequence update: June 1, 2003
    Last modified: July 22, 2015
    This is version 73 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Reaction mechanism is a simple extension of the two-step reaction catalyzed by other members of the family: Lys-184 initiates the reaction by abstraction of the alpha-proton to generate a Mg2+-stabilized enediolate intermediate, and the vinylogous beta-elimination of the 3-OH group is general acid-catalyzed by the His-322, accomplishing the anti-elimination of water. The replacement of the leaving group by solvent-derived hydrogen is stereo-random, suggesting that the enol tautomer of oxaloacetate is the product (PubMed:17144653).1 Publication

    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

    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.