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Protein

Isocitrate lyase

Gene

aceA

Organism
Hyphomicrobium methylovorum
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the metabolic adaptation in response to environmental changes. Catalyzes the reversible formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle during growth on fatty acid substrates. May be involved in the assimilation of one-carbon compounds via the isocitrate lyase-positive serine pathway.1 Publication

Catalytic activityi

Isocitrate = succinate + glyoxylate.1 Publication

Cofactori

Mg2+1 PublicationNote: Can also use Mn2+.1 Publication

Enzyme regulationi

In the presence of magnesium, inhibited by oxalate, potassium cyanide, manganese, silver, cadmium and to a lesser extent by succinate, glycolate, iodoacetamide, DL-penicillamine, aluminum, sodium, potassium, lithium and strontium.1 Publication

Kineticsi

  1. KM=0.51 mM for D-isocitrate1 Publication

    pH dependencei

    Optimum pH is 7.5. The enzyme is stable when incubated for 15 min at 30 degrees Celsius at pH 7.5-9.1 Publication

    Temperature dependencei

    Optimum temperature is 45 degrees Celsius. Loss of activity is 0%, 16%, 30%, 82% and 100% when incubated at 25, 30, 40, 50 and 60 degrees Celsius for 30 min, respectively.1 Publication

    Pathway:iglyoxylate cycle

    This protein is involved in step 1 of the subpathway that synthesizes (S)-malate from isocitrate.1 Publication
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Isocitrate lyase (aceA)
    2. no protein annotated in this organism
    This subpathway is part of the pathway glyoxylate cycle, which is itself part of Carbohydrate metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes (S)-malate from isocitrate, the pathway glyoxylate cycle and in Carbohydrate metabolism.

    Pathway:iformaldehyde assimilation via serine pathway

    This protein is involved in the pathway formaldehyde assimilation via serine pathway, which is part of One-carbon metabolism.1 Publication
    View all proteins of this organism that are known to be involved in the pathway formaldehyde assimilation via serine pathway and in One-carbon metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi187 – 1871MagnesiumBy similarity
    Active sitei225 – 2251Proton acceptorBy similarity
    Binding sitei458 – 4581SubstrateBy similarity

    GO - Molecular functioni

    • isocitrate lyase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB
    • transition metal ion binding Source: UniProtKB

    GO - Biological processi

    • glyoxylate cycle Source: UniProtKB
    • tricarboxylic acid cycle Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Glyoxylate bypass, Tricarboxylic acid cycle

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciRETL1328306-WGS:GSTH-5154-MONOMER.
    UniPathwayiUPA00703; UER00719.
    UPA00927.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isocitrate lyase1 Publication (EC:4.1.3.11 Publication)
    Short name:
    ICL1 Publication
    Alternative name(s):
    Isocitrase1 Publication
    Isocitratase1 Publication
    Gene namesi
    Name:aceABy similarity
    Synonyms:icl1 Publication
    OrganismiHyphomicrobium methylovorum
    Taxonomic identifieri84 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesHyphomicrobiaceaeHyphomicrobium

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 540539Isocitrate lyase1 PublicationPRO_0000389621Add
    BLAST

    Proteomic databases

    PRIDEiO50078.

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliO50078.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni103 – 1053Substrate bindingBy similarity
    Regioni226 – 2272Substrate bindingBy similarity
    Regioni385 – 3895Substrate bindingBy similarity

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.20.20.60. 3 hits.
    InterProiIPR006254. Isocitrate_lyase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PANTHERiPTHR21631:SF3. PTHR21631:SF3. 1 hit.
    PfamiPF00463. ICL. 3 hits.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 2 hits.

    Sequencei

    Sequence statusi: Complete.

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

    O50078-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAHKKTYSQL RSELLARYPV GLTKGGVSID DIVQLRLQSP YESHLDVARA
    60 70 80 90 100
    MASVMRADMA AYDRDTGKFT QSLGCWSGFH AQQMIKAVKR LRGTTKGAYV
    110 120 130 140 150
    YLSGWMVAGL RNRWGHLPDQ SMHEKTSVVD LIEEIYVSLR QADEVALNDL
    160 170 180 190 200
    FNELKDARAK GATNKACEEI ISRIDGFESH VVPIIADIDA GFGNEHATYL
    210 220 230 240 250
    LAKEMIKAGA CCLQIENQVS DAKQCGHQDG KVTVPREDFI EKLRACRLAF
    260 270 280 290 300
    EELGVDDGVI VARTDSLGAS LTQKIPVSQQ AGDFASSYIK WLKTEPITDA
    310 320 330 340 350
    NPLSEGELAI WQSGNFARPI RMPNGLFSFR EGTGRARVIE DCIASLKDGD
    360 370 380 390 400
    ADLIWIETDT PNVDEIASMV AEIRKQVPDA KLVYNNSPSF NWTLNLRKQV
    410 420 430 440 450
    RAQWISEGKI AEADYPDGTA LMSAQYDTSE LGREADDRLR QFQVDISARA
    460 470 480 490 500
    GVFHNLITLP TFHLTAKSTD ELSHGYFGED RMLAYVATVQ REEIRRSISA
    510 520 530 540
    VRHQHEVGSD LGDTFKEMVS GDRALKAGGA HNTMNQFAAE
    Length:540
    Mass (Da):59,898
    Last modified:June 1, 1998 - v1
    Checksum:iF289F07879534A7B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB004651 Genomic DNA. Translation: BAA23678.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB004651 Genomic DNA. Translation: BAA23678.1.

    3D structure databases

    ProteinModelPortaliO50078.
    ModBaseiSearch...
    MobiDBiSearch...

    Proteomic databases

    PRIDEiO50078.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00703; UER00719.
    UPA00927.
    BioCyciRETL1328306-WGS:GSTH-5154-MONOMER.

    Family and domain databases

    Gene3Di3.20.20.60. 3 hits.
    InterProiIPR006254. Isocitrate_lyase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PANTHERiPTHR21631:SF3. PTHR21631:SF3. 1 hit.
    PfamiPF00463. ICL. 3 hits.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 2 hits.
    ProtoNetiSearch...

    Publicationsi

    1. "Characterization, gene cloning and expression of isocitrate lyase involved in the assimilation of one-carbon compounds in Hyphomicrobium methylovorum GM2."
      Tanaka Y., Yoshida T., Watanabe K., Izumi Y., Mitsunaga T.
      Eur. J. Biochem. 249:820-825(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-20, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, SUBUNIT.
      Strain: GM2.

    Entry informationi

    Entry nameiACEA_HYPME
    AccessioniPrimary (citable) accession number: O50078
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 2009
    Last sequence update: June 1, 1998
    Last modified: April 29, 2015
    This is version 65 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.