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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)DescriptionActionsGraphical viewLength
    Binding sitei21Substrate1
    Binding sitei55Substrate1
    Sitei55Transition state stabilizer1
    Binding sitei102Substrate1
    Binding sitei156Substrate1
    Binding sitei182Substrate1
    Sitei182Transition state stabilizer1
    Active sitei184acceptor1 Publication1
    Metal bindingi213Magnesium1 Publication1
    Metal bindingi239Magnesium1 Publication1
    Binding sitei239Substrate1
    Metal bindingi265Magnesium1 Publication1
    Binding sitei265Substrate1
    Sitei292Increases basicity of active site His1
    Active sitei322Proton donor/acceptor1 Publication1
    Binding sitei322Substrate1
    Sitei341Transition state stabilizer1

    GO - Molecular functioni

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

    GO - Biological processi

    • metabolic process Source: InterPro
    • protein homooligomerization Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    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
    Proteomesi
    • UP000002526 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi102K → A or M: Loss of dehydration activity. 1 Publication1
    Mutagenesisi184K → A: Loss of dehydration activity. 1 Publication1
    Mutagenesisi184K → R: Reduced dehydration activity. 1 Publication1
    Mutagenesisi322H → N: Decreased but measurable dehydration activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004304431 – 389D(-)-tartrate dehydrataseAdd BLAST389

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.1 Publication

    Protein-protein interaction databases

    STRINGi224911.bll6730.

    Structurei

    Secondary structure

    1389
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 14Combined sources10
    Beta strandi30 – 41Combined sources12
    Beta strandi43 – 52Combined sources10
    Helixi61 – 66Combined sources6
    Helixi68 – 73Combined sources6
    Helixi77 – 79Combined sources3
    Beta strandi85 – 88Combined sources4
    Helixi90 – 97Combined sources8
    Turni98 – 100Combined sources3
    Helixi108 – 128Combined sources21
    Helixi132 – 139Combined sources8
    Beta strandi147 – 153Combined sources7
    Helixi163 – 174Combined sources12
    Turni175 – 177Combined sources3
    Beta strandi179 – 184Combined sources6
    Beta strandi186 – 188Combined sources3
    Helixi190 – 204Combined sources15
    Turni205 – 207Combined sources3
    Beta strandi209 – 213Combined sources5
    Helixi220 – 230Combined sources11
    Beta strandi236 – 239Combined sources4
    Helixi247 – 253Combined sources7
    Turni254 – 256Combined sources3
    Beta strandi261 – 263Combined sources3
    Helixi270 – 279Combined sources10
    Turni284 – 286Combined sources3
    Turni293 – 297Combined sources5
    Helixi299 – 311Combined sources13
    Helixi316 – 318Combined sources3
    Helixi326 – 335Combined sources10
    Beta strandi340 – 342Combined sources3
    Turni348 – 350Combined sources3
    Beta strandi363 – 365Combined sources3
    Helixi374 – 376Combined sources3
    Helixi378 – 385Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiQ89FH0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ89FH0.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni182 – 184Substrate binding3
    Regioni213 – 215Substrate binding3
    Regioni341 – 343Substrate binding3

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CMJ. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000257327.
    InParanoidiQ89FH0.
    OMAiVKMKIGG.
    OrthoDBiPOG091H0MVB.
    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.
    PfamiPF13378. MR_MLE_C. 1 hit.
    [Graphical view]
    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. NZ_CP011360.1.

    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. NZ_CP011360.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiQ89FH0.
    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

    eggNOGiENOG4105CMJ. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000257327.
    InParanoidiQ89FH0.
    OMAiVKMKIGG.
    OrthoDBiPOG091H0MVB.
    PhylomeDBiQ89FH0.

    Enzyme and pathway databases

    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.
    PfamiPF13378. MR_MLE_C. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 81 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

    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 one 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.