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Protein

2-methylisocitrate lyase

Gene

prpB

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate via an alpha-carboxy-carbanion intermediate.UniRule annotation3 Publications

Miscellaneous

In vitro, dithiothreitol (DTT) or reduced glutathione (GSH) are required for optimal activity.1 Publication

Catalytic activityi

(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.UniRule annotation2 Publications

Cofactori

Mg2+UniRule annotation2 Publications

Kineticsi

Kcat is 74 sec(-1) for 2-methylisocitrate lyase with 2-methylisocitrate as substrate.1 Publication
  1. KM=18 µM for 2-methylisocitrate1 Publication

    pH dependencei

    Optimum pH is 7.5.1 Publication

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius.1 Publication

    Pathwayi: propanoate degradation

    This protein is involved in the pathway propanoate degradation, which is part of Organic acid metabolism.UniRule annotation1 Publication
    View all proteins of this organism that are known to be involved in the pathway propanoate degradation and in Organic acid metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi85Magnesium1 Publication1
    Metal bindingi87MagnesiumUniRule annotation1
    Binding sitei158Substrate1 Publication1
    Binding sitei188SubstrateUniRule annotation1
    Binding sitei241SubstrateUniRule annotation1
    Binding sitei270SubstrateUniRule annotation1

    GO - Molecular functioni

    • magnesium ion binding Source: UniProtKB
    • methylisocitrate lyase activity Source: UniProtKB

    GO - Biological processi

    Keywordsi

    Molecular functionLyase
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-66
    SENT99287:G1FZD-373-MONOMER
    UniPathwayi
    UPA00946

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-methylisocitrate lyase1 Publication (EC:4.1.3.302 Publications)
    Short name:
    2-MIC1 Publication
    Short name:
    MICL1 Publication
    Alternative name(s):
    (2R,3S)-2-methylisocitrate lyaseUniRule annotation
    Gene namesi
    Name:prpB1 Publication
    Ordered Locus Names:STM0368
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene are unable to accumulate 2-methylcitrate and 2-methyl-cis-aconitate.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi58D → A: Inactive. Retains the same oligomeric state of the wild-type. 1 Publication1
    Mutagenesisi121K → A: 1000-fold decrease in the catalytic efficiency. Retains the same oligomeric state of the wild-type. 1 Publication1
    Mutagenesisi122R → K: 2-fold decrease in the catalytic efficiency. Retains the same oligomeric state of the wild-type. 1 Publication1
    Mutagenesisi123C → A: Inactive. Retains the same oligomeric state of the wild-type. 1 Publication1
    Mutagenesisi125H → A: 750-fold decrease in the catalytic efficiency. Retains the same oligomeric state of the wild-type. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemovedCurated
    ChainiPRO_00000688162 – 2952-methylisocitrate lyaseAdd BLAST294

    Proteomic databases

    PaxDbiQ56062
    PRIDEiQ56062

    Interactioni

    Subunit structurei

    Homotetramer; dimer of dimers.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi99287.STM0368

    Structurei

    Secondary structure

    1295
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliQ56062
    SMRiQ56062
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ56062

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni45 – 47Substrate binding1 Publication3
    Regioni123 – 124Substrate bindingUniRule annotation2
    Regioni210 – 212Substrate bindingUniRule annotation3

    Sequence similaritiesi

    Belongs to the isocitrate lyase/PEP mutase superfamily. Methylisocitrate lyase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CR4 Bacteria
    COG2513 LUCA
    HOGENOMiHOG000220041
    KOiK03417
    OMAiFGQTELW
    PhylomeDBiQ56062

    Family and domain databases

    HAMAPiMF_01939 PrpB, 1 hit
    InterProiView protein in InterPro
    IPR018523 Isocitrate_lyase_ph_CS
    IPR012695 PrpB
    IPR015813 Pyrv/PenolPyrv_Kinase-like_dom
    SUPFAMiSSF51621 SSF51621, 1 hit
    TIGRFAMsiTIGR02317 prpB, 1 hit
    PROSITEiView protein in PROSITE
    PS00161 ISOCITRATE_LYASE, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q56062-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MSLHSPGQAF RAALAKENPL QIVGAINANH ALLAQRAGYQ AIYLSGGGVA
    60 70 80 90 100
    AGSLGLPDLG ISTLDDVLTD IRRITDVCPL PLLVDADIGF GSSAFNVART
    110 120 130 140 150
    VKSIAKAGAA ALHIEDQVGA KRCGHRPNKA IVSKEEMVDR IRAAVDARTD
    160 170 180 190 200
    PNFVIMARTD ALAVEGLEAA LDRAQAYVDA GADMLFPEAI TELSMYRRFA
    210 220 230 240 250
    DVAQVPILAN ITEFGATPLF TTDELRSAHV AMALYPLSAF RAMNRAAEKV
    260 270 280 290
    YTVLRQEGTQ KNVIDIMQTR NELYESINYY QFEEKLDALY RNKKS
    Length:295
    Mass (Da):32,000
    Last modified:January 23, 2007 - v3
    Checksum:i08AD38D071B98F1D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U51879 Genomic DNA Translation: AAC44814.1
    AE006468 Genomic DNA Translation: AAL19322.1
    RefSeqiNP_459363.1, NC_003197.2
    WP_000052224.1, NC_003197.2

    Genome annotation databases

    EnsemblBacteriaiAAL19322; AAL19322; STM0368
    GeneIDi1251887
    KEGGistm:STM0368
    PATRICifig|99287.12.peg.390

    Similar proteinsi

    Entry informationi

    Entry nameiPRPB_SALTY
    AccessioniPrimary (citable) accession number: Q56062
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 23, 2007
    Last modified: March 28, 2018
    This is version 116 of the entry and version 3 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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