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Protein

2-methylisocitrate lyase

Gene

prpB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 annotation2 Publications

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation3 Publications

Kineticsi

Kcat is 12 sec(-1) for methylisocitrate lyase with threo-2-methylisocitrate as substrate (mixture of (2R,3S)- and (2S,3R)-2-methylisocitrate at pH 7 and 30 degrees Celsius).1 Publication
  1. KM=35 µM for magnesium2 Publications
  2. KM=19 µM for threo-2-methylisocitrate (a mixture of (2R,3S)- and (2S,3R)-2-methylisocitrate in presence of 2 mM magnesium at pH 7 and 30 degrees Celsius)2 Publications

    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 bindingi85MagnesiumUniRule annotation2 Publications1
    Metal bindingi87MagnesiumUniRule annotation2 Publications1
    Binding sitei158SubstrateUniRule annotation1 Publication1
    Binding sitei188SubstrateUniRule annotation1 Publication1
    Binding sitei241SubstrateUniRule annotation1 Publication1
    Binding sitei270SubstrateUniRule annotation1 Publication1

    GO - Molecular functioni

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

    GO - Biological processi

    • propionate catabolic process, 2-methylcitrate cycle Source: EcoCyc

    Keywordsi

    Molecular functionLyase
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G6196-MONOMER.
    MetaCyc:G6196-MONOMER.
    BRENDAi4.1.3.30. 2026.
    UniPathwayiUPA00946.

    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 lyase1 Publication
    Gene namesi
    Name:prpBUniRule annotation
    Synonyms:yahQ
    Ordered Locus Names:b0331, JW0323
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13601. prpB.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi123C → S: Inactive. 1 Publication1

    Chemistry databases

    DrugBankiDB01727. Isocitric Acid.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved2 Publications
    ChainiPRO_00000688152 – 2962-methylisocitrate lyaseAdd BLAST295

    Proteomic databases

    PaxDbiP77541.
    PRIDEiP77541.

    Interactioni

    Subunit structurei

    Homotetramer; dimer of dimers.UniRule annotation2 Publications

    Protein-protein interaction databases

    BioGridi4259808. 9 interactors.
    IntActiP77541. 12 interactors.
    STRINGi316407.85674474.

    Structurei

    Secondary structure

    1296
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 16Combined sources11
    Beta strandi17 – 24Combined sources8
    Helixi28 – 36Combined sources9
    Beta strandi42 – 44Combined sources3
    Helixi46 – 51Combined sources6
    Turni52 – 54Combined sources3
    Beta strandi58 – 60Combined sources3
    Helixi64 – 77Combined sources14
    Beta strandi82 – 85Combined sources4
    Beta strandi90 – 93Combined sources4
    Helixi94 – 107Combined sources14
    Beta strandi110 – 115Combined sources6
    Beta strandi126 – 128Combined sources3
    Helixi134 – 147Combined sources14
    Beta strandi153 – 159Combined sources7
    Helixi162 – 165Combined sources4
    Helixi167 – 179Combined sources13
    Beta strandi183 – 187Combined sources5
    Helixi193 – 203Combined sources11
    Beta strandi207 – 210Combined sources4
    Beta strandi213 – 217Combined sources5
    Helixi222 – 227Combined sources6
    Beta strandi231 – 237Combined sources7
    Helixi238 – 257Combined sources20
    Beta strandi258 – 260Combined sources3
    Helixi261 – 266Combined sources6
    Helixi270 – 276Combined sources7
    Helixi279 – 287Combined sources9

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1MUMX-ray1.90A/B2-296[»]
    1MZXmodel-A3-290[»]
    1OQFX-ray1.93A/B2-296[»]
    1XG3X-ray1.90A/B/C/D2-296[»]
    1XG4X-ray1.60A/B/C/D2-296[»]
    ProteinModelPortaliP77541.
    SMRiP77541.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77541.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni45 – 47Substrate bindingUniRule annotation1 Publication3
    Regioni123 – 124Substrate bindingUniRule annotation1 Publication2
    Regioni210 – 212Substrate bindingUniRule annotation1 Publication3

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105CR4. Bacteria.
    COG2513. LUCA.
    HOGENOMiHOG000220041.
    InParanoidiP77541.
    KOiK03417.
    PhylomeDBiP77541.

    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.

    P77541-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSLHSPGKAF RAALTKENPL QIVGTINANH ALLAQRAGYQ AIYLSGGGVA
    60 70 80 90 100
    AGSLGLPDLG ISTLDDVLTD IRRITDVCSL PLLVDADIGF GSSAFNVART
    110 120 130 140 150
    VKSMIKAGAA GLHIEDQVGA KRCGHRPNKA IVSKEEMVDR IRAAVDAKTD
    160 170 180 190 200
    PDFVIMARTD ALAVEGLDAA IERAQAYVEA GAEMLFPEAI TELAMYRQFA
    210 220 230 240 250
    DAVQVPILAN ITEFGATPLF TTDELRSAHV AMALYPLSAF RAMNRAAEHV
    260 270 280 290
    YNVLRQEGTQ KSVIDTMQTR NELYESINYY QYEEKLDNLF ARSQVK
    Length:296
    Mass (Da):32,135
    Last modified:January 23, 2007 - v3
    Checksum:i2AA3DAE3F84472F3
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U73857 Genomic DNA. Translation: AAB18055.1.
    U00096 Genomic DNA. Translation: AAC73434.1.
    AP009048 Genomic DNA. Translation: BAE76114.1.
    PIRiC64760.
    RefSeqiNP_414865.1. NC_000913.3.
    WP_000052206.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73434; AAC73434; b0331.
    BAE76114; BAE76114; BAE76114.
    GeneIDi944990.
    KEGGiecj:JW0323.
    eco:b0331.
    PATRICifig|1411691.4.peg.1945.

    Similar proteinsi

    Entry informationi

    Entry nameiPRPB_ECOLI
    AccessioniPrimary (citable) accession number: P77541
    Secondary accession number(s): Q2MC92
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 23, 2007
    Last modified: August 30, 2017
    This is version 137 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, Direct protein sequencing, 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