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Protein

Galactarate dehydratase (L-threo-forming)

Gene

garD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of galactarate to form 5-dehydro-4-deoxy-D-glucarate.UniRule annotation1 Publication

Catalytic activityi

Galactarate = (2R,3S)-2,3-dihydroxy-5-oxohexanedioate + H2O.UniRule annotation1 Publication

Kineticsi

kcat is 22 sec(-1).1 Publication

  1. KM=800 µM for galactarate1 Publication

    Pathwayi: galactarate degradation

    This protein is involved in step 1 of the subpathway that synthesizes D-glycerate from galactarate.UniRule annotation1 Publication
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. Galactarate dehydratase (L-threo-forming) (garD)
    2. 5-keto-4-deoxy-D-glucarate aldolase (garL)
    3. 2-hydroxy-3-oxopropionate reductase (garR)
    This subpathway is part of the pathway galactarate degradation, which is itself part of Carbohydrate acid metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glycerate from galactarate, the pathway galactarate degradation and in Carbohydrate acid metabolism.

    GO - Molecular functioni

    • galactarate dehydratase activity Source: EcoCyc

    GO - Biological processi

    • galactarate catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Enzyme and pathway databases

    BioCyciEcoCyc:GALACTARDEHYDRA-MONOMER.
    ECOL316407:JW3097-MONOMER.
    MetaCyc:GALACTARDEHYDRA-MONOMER.
    RETL1328306-WGS:GSTH-507-MONOMER.
    UniPathwayiUPA00565; UER00629.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Galactarate dehydratase (L-threo-forming)1 PublicationUniRule annotation (EC:4.2.1.42UniRule annotation1 Publication)
    Short name:
    GalcD1 PublicationUniRule annotation
    Gene namesi
    Name:garD1 PublicationUniRule annotation
    Synonyms:yhaG
    Ordered Locus Names:b3128, JW3097
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12522. garD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 523523Galactarate dehydratase (L-threo-forming)PRO_0000172285Add
    BLAST

    Proteomic databases

    PaxDbiP39829.
    PRIDEiP39829.

    Expressioni

    Inductioni

    Induced by galactarate, D-glucarate and D-glycerate.1 Publication

    Interactioni

    Protein-protein interaction databases

    BioGridi4259485. 17 interactions.
    IntActiP39829. 5 interactions.
    STRINGi511145.b3128.

    Structurei

    Secondary structure

    1
    523
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi14 – 163Combined sources
    Beta strandi23 – 297Combined sources
    Beta strandi54 – 585Combined sources
    Beta strandi65 – 684Combined sources
    Beta strandi71 – 788Combined sources
    Helixi88 – 903Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3LAZX-ray1.92A/B6-96[»]
    ProteinModelPortaliP39829.
    SMRiP39829. Positions 1-95.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39829.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the UxaA family.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiENOG4105CTX. Bacteria.
    COG2721. LUCA.
    HOGENOMiHOG000219063.
    InParanoidiP39829.
    KOiK01708.
    OMAiHSYGCGV.
    PhylomeDBiP39829.

    Family and domain databases

    HAMAPiMF_02031. Galactar_dehydrat. 1 hit.
    InterProiIPR007392. Gal/Altron_deHydtase_C.
    IPR017654. GarD-like.
    IPR032893. GarD_Enterobacteriaceae.
    IPR013974. SAF.
    [Graphical view]
    PfamiPF04295. GD_AH_C. 1 hit.
    PF08666. SAF. 1 hit.
    [Graphical view]
    SMARTiSM00858. SAF. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR03248. galactar-dH20. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P39829-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MANIEIRQET PTAFYIKVHD TDNVAIIVND NGLKAGTRFP DGLELIEHIP
    60 70 80 90 100
    QGHKVALLDI PANGEIIRYG EVIGYAVRAI PRGSWIDESM VVLPEAPPLH
    110 120 130 140 150
    TLPLATKVPE PLPPLEGYTF EGYRNADGSV GTKNLLGITT SVHCVAGVVD
    160 170 180 190 200
    YVVKIIERDL LPKYPNVDGV VGLNHLYGCG VAINAPAAVV PIRTIHNISL
    210 220 230 240 250
    NPNFGGEVMV IGLGCEKLQP ERLLTGTDDV QAIPVESASI VSLQDEKHVG
    260 270 280 290 300
    FQSMVEDILQ IAERHLQKLN QRQRETCPAS ELVVGMQCGG SDAFSGVTAN
    310 320 330 340 350
    PAVGYASDLL VRCGATVMFS EVTEVRDAIH LLTPRAVNEE VGKRLLEEME
    360 370 380 390 400
    WYDNYLNMGK TDRSANPSPG NKKGGLANVV EKALGSIAKS GKSAIVEVLS
    410 420 430 440 450
    PGQRPTKRGL IYAATPASDF VCGTQQVASG ITVQVFTTGR GTPYGLMAVP
    460 470 480 490 500
    VIKMATRTEL ANRWFDLMDI NAGTIATGEE TIEEVGWKLF HFILDVASGK
    510 520
    KKTFSDQWGL HNQLAVFNPA PVT
    Length:523
    Mass (Da):56,402
    Last modified:November 1, 1995 - v2
    Checksum:i919BCC8B49411BB0
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA57931.1.
    U00096 Genomic DNA. Translation: AAC76162.1.
    AP009048 Genomic DNA. Translation: BAE77175.1.
    M30178 Genomic DNA. No translation available.
    PIRiD65102.
    RefSeqiNP_417597.1. NC_000913.3.
    WP_001273753.1. NZ_CP014272.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76162; AAC76162; b3128.
    BAE77175; BAE77175; BAE77175.
    GeneIDi947641.
    KEGGiecj:JW3097.
    eco:b3128.
    PATRICi32121672. VBIEscCol129921_3222.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA57931.1.
    U00096 Genomic DNA. Translation: AAC76162.1.
    AP009048 Genomic DNA. Translation: BAE77175.1.
    M30178 Genomic DNA. No translation available.
    PIRiD65102.
    RefSeqiNP_417597.1. NC_000913.3.
    WP_001273753.1. NZ_CP014272.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3LAZX-ray1.92A/B6-96[»]
    ProteinModelPortaliP39829.
    SMRiP39829. Positions 1-95.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259485. 17 interactions.
    IntActiP39829. 5 interactions.
    STRINGi511145.b3128.

    Proteomic databases

    PaxDbiP39829.
    PRIDEiP39829.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76162; AAC76162; b3128.
    BAE77175; BAE77175; BAE77175.
    GeneIDi947641.
    KEGGiecj:JW3097.
    eco:b3128.
    PATRICi32121672. VBIEscCol129921_3222.

    Organism-specific databases

    EchoBASEiEB2413.
    EcoGeneiEG12522. garD.

    Phylogenomic databases

    eggNOGiENOG4105CTX. Bacteria.
    COG2721. LUCA.
    HOGENOMiHOG000219063.
    InParanoidiP39829.
    KOiK01708.
    OMAiHSYGCGV.
    PhylomeDBiP39829.

    Enzyme and pathway databases

    UniPathwayiUPA00565; UER00629.
    BioCyciEcoCyc:GALACTARDEHYDRA-MONOMER.
    ECOL316407:JW3097-MONOMER.
    MetaCyc:GALACTARDEHYDRA-MONOMER.
    RETL1328306-WGS:GSTH-507-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP39829.
    PROiP39829.

    Family and domain databases

    HAMAPiMF_02031. Galactar_dehydrat. 1 hit.
    InterProiIPR007392. Gal/Altron_deHydtase_C.
    IPR017654. GarD-like.
    IPR032893. GarD_Enterobacteriaceae.
    IPR013974. SAF.
    [Graphical view]
    PfamiPF04295. GD_AH_C. 1 hit.
    PF08666. SAF. 1 hit.
    [Graphical view]
    SMARTiSM00858. SAF. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR03248. galactar-dH20. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGARD_ECOLI
    AccessioniPrimary (citable) accession number: P39829
    Secondary accession number(s): Q2M981
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 1, 1995
    Last modified: September 7, 2016
    This is version 111 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.