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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

Manual assertion based on experiment ini

  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

    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.
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    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)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
    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
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 16Combined sources11
    Beta strandi17 – 24Combined sources8
    Helixi28 – 37Combined sources10
    Beta strandi40 – 44Combined sources5
    Helixi46 – 51Combined sources6
    Beta strandi58 – 60Combined sources3
    Helixi64 – 77Combined sources14
    Beta strandi82 – 85Combined sources4
    Beta strandi90 – 93Combined sources4
    Helixi94 – 106Combined sources13
    Beta strandi110 – 115Combined sources6
    Helixi134 – 147Combined sources14
    Beta strandi153 – 159Combined sources7
    Helixi161 – 165Combined sources5
    Helixi167 – 179Combined sources13
    Beta strandi183 – 187Combined sources5
    Helixi193 – 203Combined sources11
    Beta strandi207 – 210Combined sources4
    Beta strandi213 – 217Combined sources5
    Helixi222 – 227Combined sources6
    Beta strandi232 – 237Combined sources6
    Helixi238 – 257Combined sources20
    Beta strandi258 – 260Combined sources3
    Helixi261 – 266Combined sources6
    Helixi270 – 276Combined sources7
    Helixi279 – 285Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1O5QX-ray2.30A/B/C/D2-295[»]
    1UJQX-ray2.10A/B/C/D2-295[»]
    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

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1O5QX-ray2.30A/B/C/D2-295[»]
    1UJQX-ray2.10A/B/C/D2-295[»]
    ProteinModelPortaliQ56062.
    SMRiQ56062.
    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.

    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: November 2, 2016
    This is version 109 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.