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Protein

2-methylisocitrate lyase

Gene

prpB

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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 annotation3 Publications

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)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi85 – 851Magnesium1 Publication
    Metal bindingi87 – 871MagnesiumUniRule annotation
    Binding sitei158 – 1581Substrate1 Publication
    Binding sitei188 – 1881SubstrateUniRule annotation
    Binding sitei241 – 2411SubstrateUniRule annotation
    Binding sitei270 – 2701SubstrateUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

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

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-66.
    SENT99287:GCTI-369-MONOMER.
    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 lyaseUniRule annotation
    Gene namesi
    Name:prpB1 Publication
    Ordered Locus Names:STM0368
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi58 – 581D → A: Inactive. Retains the same oligomeric state of the wild-type. 1 Publication
    Mutagenesisi121 – 1211K → A: 1000-fold decrease in the catalytic efficiency. Retains the same oligomeric state of the wild-type. 1 Publication
    Mutagenesisi122 – 1221R → K: 2-fold decrease in the catalytic efficiency. Retains the same oligomeric state of the wild-type. 1 Publication
    Mutagenesisi123 – 1231C → A: Inactive. Retains the same oligomeric state of the wild-type. 1 Publication
    Mutagenesisi125 – 1251H → A: 750-fold decrease in the catalytic efficiency. Retains the same oligomeric state of the wild-type. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini2 – 2952942-methylisocitrate lyasePRO_0000068816Add
    BLAST

    Proteomic databases

    PaxDbiQ56062.
    PRIDEiQ56062.

    Interactioni

    Subunit structurei

    Homotetramer; dimer of dimers.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi99287.STM0368.

    Structurei

    Secondary structure

    1
    295
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1611Combined sources
    Beta strandi17 – 248Combined sources
    Helixi28 – 3710Combined sources
    Beta strandi40 – 445Combined sources
    Helixi46 – 516Combined sources
    Beta strandi58 – 603Combined sources
    Helixi64 – 7714Combined sources
    Beta strandi82 – 854Combined sources
    Beta strandi90 – 934Combined sources
    Helixi94 – 10613Combined sources
    Beta strandi110 – 1156Combined sources
    Helixi134 – 14714Combined sources
    Beta strandi153 – 1597Combined sources
    Helixi161 – 1655Combined sources
    Helixi167 – 17913Combined sources
    Beta strandi183 – 1875Combined sources
    Helixi193 – 20311Combined sources
    Beta strandi207 – 2104Combined sources
    Beta strandi213 – 2175Combined sources
    Helixi222 – 2276Combined sources
    Beta strandi232 – 2376Combined sources
    Helixi238 – 25720Combined sources
    Beta strandi258 – 2603Combined sources
    Helixi261 – 2666Combined sources
    Helixi270 – 2767Combined sources
    Helixi279 – 2857Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1O5QX-ray2.30A/B/C/D2-295[»]
    1UJQX-ray2.10A/B/C/D2-295[»]
    ProteinModelPortaliQ56062.
    SMRiQ56062. Positions 2-290.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ56062.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni45 – 473Substrate binding1 Publication
    Regioni123 – 1242Substrate bindingUniRule annotation
    Regioni210 – 2123Substrate bindingUniRule annotation

    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

    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.

    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_003197.1.
    WP_000052224.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL19322; AAL19322; STM0368.
    GeneIDi1251887.
    KEGGistm:STM0368.
    PATRICi32379057. VBISalEnt20916_0390.

    Cross-referencesi

    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_003197.1.
    WP_000052224.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1O5QX-ray2.30A/B/C/D2-295[»]
    1UJQX-ray2.10A/B/C/D2-295[»]
    ProteinModelPortaliQ56062.
    SMRiQ56062. Positions 2-290.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM0368.

    Proteomic databases

    PaxDbiQ56062.
    PRIDEiQ56062.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL19322; AAL19322; STM0368.
    GeneIDi1251887.
    KEGGistm:STM0368.
    PATRICi32379057. VBISalEnt20916_0390.

    Phylogenomic databases

    eggNOGiENOG4105CR4. Bacteria.
    COG2513. LUCA.
    HOGENOMiHOG000220041.
    KOiK03417.
    OMAiFGQTELW.
    PhylomeDBiQ56062.

    Enzyme and pathway databases

    UniPathwayiUPA00946.
    BioCyciMetaCyc:MONOMER-66.
    SENT99287:GCTI-369-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ56062.

    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_SALTY
    AccessioniPrimary (citable) accession number: Q56062
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 23, 2007
    Last modified: September 7, 2016
    This is version 107 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

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

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.