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Q89FH0

- TARD_BRADU

UniProt

Q89FH0 - TARD_BRADU

Protein

D(-)-tartrate dehydratase

Gene

tarD

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 67 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

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

    Cofactori

    Binds 1 magnesium 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

    1. catalytic activity Source: InterPro
    2. metal ion binding Source: UniProtKB-KW

    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: 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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    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.
    [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

    MSVRIVDVRE ITKPISSPIR NAYIDFTKMT TSLVAVVTDV VREGKRVVGY    50
    GFNSNGRYGQ GGLIRERFAS RILEADPKKL LNEAGDNLDP DKVWAAMMIN 100
    EKPGGHGERS VAVGTIDMAV WDAVAKIAGK PLFRLLAERH GVKANPRVFV 150
    YAAGGYYYPG KGLSMLRGEM RGYLDRGYNV VKMKIGGAPI EEDRMRIEAV 200
    LEEIGKDAQL AVDANGRFNL ETGIAYAKML RDYPLFWYEE VGDPLDYALQ 250
    AALAEFYPGP MATGENLFSH QDARNLLRYG GMRPDRDWLQ FDCALSYGLC 300
    EYQRTLEVLK THGWSPSRCI PHGGHQMSLN IAAGLGLGGN ESYPDLFQPY 350
    GGFPDGVRVE NGHITMPDLP GIGFEGKSDL YKEMKALAE 389
    Length:389
    Mass (Da):43,058
    Last modified:June 1, 2003 - v1
    Checksum:i0FE177A59AB2F82C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000040 Genomic DNA. Translation: BAC51995.1.
    RefSeqiNP_773370.1. NC_004463.1.

    Genome annotation databases

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

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000040 Genomic DNA. Translation: BAC51995.1 .
    RefSeqi NP_773370.1. NC_004463.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1TZZ X-ray 1.86 A/B 1-389 [» ]
    2DW6 X-ray 2.30 A/B/C/D 1-389 [» ]
    2DW7 X-ray 2.50 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P 1-389 [» ]
    ProteinModelPortali Q89FH0.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224911.bll6730.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAC51995 ; BAC51995 ; BAC51995 .
    GeneIDi 1050053.
    KEGGi bja:bll6730.
    PATRICi 21197324. VBIBraJap65052_6896.

    Phylogenomic databases

    HOGENOMi HOG000257327.
    OrthoDBi EOG6Q2SGK.
    PhylomeDBi Q89FH0.

    Enzyme and pathway databases

    BioCyci BJAP224911:GJEJ-6781-MONOMER.
    SABIO-RK Q89FH0.

    Miscellaneous databases

    EvolutionaryTracei Q89FH0.

    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.
    IPR013342. Mandelate_racemase_C.
    IPR001354. MR_MLE.
    [Graphical view ]
    PANTHERi PTHR13794. PTHR13794. 1 hit.
    SMARTi SM00922. MR_MLE. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 67 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