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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)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi85 – 851MagnesiumUniRule annotation2 Publications
    Metal bindingi87 – 871MagnesiumUniRule annotation2 Publications
    Binding sitei158 – 1581SubstrateUniRule annotation1 Publication
    Binding sitei188 – 1881SubstrateUniRule annotation1 Publication
    Binding sitei241 – 2411SubstrateUniRule annotation1 Publication
    Binding sitei270 – 2701SubstrateUniRule annotation1 Publication

    GO - Molecular functioni

    GO - Biological processi

    • glyoxylate cycle Source: GO_Central
    • propionate catabolic process, 2-methylcitrate cycle Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G6196-MONOMER.
    ECOL316407:JW0323-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13601. prpB.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi123 – 1231C → S: Inactive. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved2 Publications
    Chaini2 – 2962952-methylisocitrate lyasePRO_0000068815Add
    BLAST

    Proteomic databases

    EPDiP77541.
    PaxDbiP77541.
    PRIDEiP77541.

    Interactioni

    Subunit structurei

    Homotetramer; dimer of dimers.UniRule annotation2 Publications

    Protein-protein interaction databases

    BioGridi4259808. 9 interactions.
    IntActiP77541. 12 interactions.
    STRINGi511145.b0331.

    Structurei

    Secondary structure

    1
    296
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1611Combined sources
    Beta strandi17 – 248Combined sources
    Helixi28 – 369Combined sources
    Beta strandi42 – 443Combined sources
    Helixi46 – 516Combined sources
    Turni52 – 543Combined sources
    Beta strandi58 – 603Combined sources
    Helixi64 – 7714Combined sources
    Beta strandi82 – 854Combined sources
    Beta strandi90 – 934Combined sources
    Helixi94 – 10714Combined sources
    Beta strandi110 – 1156Combined sources
    Beta strandi126 – 1283Combined sources
    Helixi134 – 14714Combined sources
    Beta strandi153 – 1597Combined sources
    Helixi162 – 1654Combined sources
    Helixi167 – 17913Combined sources
    Beta strandi183 – 1875Combined sources
    Helixi193 – 20311Combined sources
    Beta strandi207 – 2104Combined sources
    Beta strandi213 – 2175Combined sources
    Helixi222 – 2276Combined sources
    Beta strandi231 – 2377Combined sources
    Helixi238 – 25720Combined sources
    Beta strandi258 – 2603Combined sources
    Helixi261 – 2666Combined sources
    Helixi270 – 2767Combined sources
    Helixi279 – 2879Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 3-291.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77541.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni45 – 473Substrate bindingUniRule annotation1 Publication
    Regioni123 – 1242Substrate bindingUniRule annotation1 Publication
    Regioni210 – 2123Substrate bindingUniRule annotation1 Publication

    Sequence similaritiesi

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

    Phylogenomic databases

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

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01939. PrpB. 1 hit.
    InterProiIPR018523. Isocitrate_lyase_ph_CS.
    IPR012695. PrpB.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    TIGRFAMsiTIGR02317. prpB. 1 hit.
    PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
    [Graphical view]

    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.
    PATRICi32115795. VBIEscCol129921_0339.

    Cross-referencesi

    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 3-291.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259808. 9 interactions.
    IntActiP77541. 12 interactions.
    STRINGi511145.b0331.

    Proteomic databases

    EPDiP77541.
    PaxDbiP77541.
    PRIDEiP77541.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73434; AAC73434; b0331.
    BAE76114; BAE76114; BAE76114.
    GeneIDi944990.
    KEGGiecj:JW0323.
    eco:b0331.
    PATRICi32115795. VBIEscCol129921_0339.

    Organism-specific databases

    EchoBASEiEB3370.
    EcoGeneiEG13601. prpB.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayiUPA00946.
    BioCyciEcoCyc:G6196-MONOMER.
    ECOL316407:JW0323-MONOMER.
    MetaCyc:G6196-MONOMER.
    BRENDAi4.1.3.30. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP77541.
    PROiP77541.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01939. PrpB. 1 hit.
    InterProiIPR018523. Isocitrate_lyase_ph_CS.
    IPR012695. PrpB.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    TIGRFAMsiTIGR02317. prpB. 1 hit.
    PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPRPB_ECOLI
    AccessioniPrimary (citable) accession number: P77541
    Secondary accession number(s): Q2MC92
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 23, 2007
    Last modified: September 7, 2016
    This is version 129 of the entry and version 3 of the sequence. [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

    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.