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P40495

- LYS12_YEAST

UniProt

P40495 - LYS12_YEAST

Protein

Homoisocitrate dehydrogenase, mitochondrial

Gene

LYS12

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Catalyzes the NAD+-dependent conversion of homoisocitrate to alpha-ketoadipate.1 Publication

    Catalytic activityi

    (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH.3 Publications

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.2 Publications

    Enzyme regulationi

    Inhibited by the reaction product NADH. Inhibited by oxalate; this is a non-competitive inhibitor.1 Publication

    Kineticsi

    The KM for homoisocitrate is lower than 10 µM.

    1. KM=1.5 mM for 2-oxoadipate1 Publication
    2. KM=330 µM for NAD+1 Publication
    3. KM=65 µM for NADH1 Publication

    pH dependencei

    Optimum pH is 8.3-8.8 for the forward reaction, and 7 for the reverse reaction.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei114 – 1141SubstrateBy similarity
    Binding sitei124 – 1241SubstrateBy similarity
    Binding sitei143 – 1431SubstrateBy similarity
    Sitei150 – 1501Critical for catalysis
    Sitei206 – 2061Critical for catalysis
    Metal bindingi243 – 2431Magnesium or manganeseBy similarity
    Binding sitei243 – 2431SubstrateBy similarity
    Metal bindingi267 – 2671Magnesium or manganeseBy similarity
    Metal bindingi271 – 2711Magnesium or manganeseBy similarity

    GO - Molecular functioni

    1. homoisocitrate dehydrogenase activity Source: SGD
    2. magnesium ion binding Source: InterPro
    3. NAD binding Source: InterPro

    GO - Biological processi

    1. lysine biosynthetic process Source: SGD
    2. lysine biosynthetic process via aminoadipic acid Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, NAD

    Enzyme and pathway databases

    BioCyciYEAST:YIL094C-MONOMER.
    UniPathwayiUPA00033; UER00030.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Homoisocitrate dehydrogenase, mitochondrial (EC:1.1.1.87)
    Short name:
    HIcDH
    Gene namesi
    Name:LYS12
    Synonyms:LYS10, LYS11
    Ordered Locus Names:YIL094C
    ORF Names:YI9910.02C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IX

    Organism-specific databases

    CYGDiYIL094c.
    SGDiS000001356. LYS12.

    Subcellular locationi

    Mitochondrion 2 Publications

    GO - Cellular componenti

    1. mitochondrion Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi150 – 1501Y → F: Strongly reduced enzyme activity. 1 Publication
    Mutagenesisi206 – 2061K → M: Strongly reduced enzyme activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 2222MitochondrionSequence AnalysisAdd
    BLAST
    Chaini23 – 371349Homoisocitrate dehydrogenase, mitochondrialPRO_0000043097Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei98 – 981Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP40495.
    PaxDbiP40495.
    PeptideAtlasiP40495.

    Expressioni

    Inductioni

    Activity is repressed 4-fold by lysine.1 Publication

    Gene expression databases

    GenevestigatoriP40495.

    Interactioni

    Protein-protein interaction databases

    BioGridi34898. 68 interactions.
    DIPiDIP-4162N.
    IntActiP40495. 90 interactions.
    MINTiMINT-491742.
    STRINGi4932.YIL094C.

    Structurei

    3D structure databases

    ProteinModelPortaliP40495.
    SMRiP40495. Positions 22-371.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0473.
    GeneTreeiENSGT00550000076087.
    HOGENOMiHOG000021111.
    KOiK05824.
    OMAiEFMGYPE.
    OrthoDBiEOG7R83BB.

    Family and domain databases

    Gene3Di3.40.718.10. 1 hit.
    InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
    IPR001804. Isocitrate/isopropylmalate_DH.
    IPR024084. IsoPropMal-DH-like_dom.
    [Graphical view]
    PANTHERiPTHR11835. PTHR11835. 1 hit.
    PfamiPF00180. Iso_dh. 1 hit.
    [Graphical view]
    PROSITEiPS00470. IDH_IMDH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P40495-1 [UniParc]FASTAAdd to Basket

    « Hide

    MFRSVATRLS ACRGLASNAA RKSLTIGLIP GDGIGKEVIP AGKQVLENLN    50
    SKHGLSFNFI DLYAGFQTFQ ETGKALPDET VKVLKEQCQG ALFGAVQSPT 100
    TKVEGYSSPI VALRREMGLF ANVRPVKSVE GEKGKPIDMV IVRENTEDLY 150
    IKIEKTYIDK ATGTRVADAT KRISEIATRR IATIALDIAL KRLQTRGQAT 200
    LTVTHKSNVL SQSDGLFREI CKEVYESNKD KYGQIKYNEQ IVDSMVYRLF 250
    REPQCFDVIV APNLYGDILS DGAAALVGSL GVVPSANVGP EIVIGEPCHG 300
    SAPDIAGKGI ANPIATIRST ALMLEFLGHN EAAQDIYKAV DANLREGSIK 350
    TPDLGGKAST QQVVDDVLSR L 371
    Length:371
    Mass (Da):40,069
    Last modified:February 1, 1995 - v1
    Checksum:i43CAFA86F75ED3C6
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z46728 Genomic DNA. Translation: CAA86700.1.
    BK006942 Genomic DNA. Translation: DAA08459.1.
    PIRiS49786.
    RefSeqiNP_012172.1. NM_001179442.1.

    Genome annotation databases

    EnsemblFungiiYIL094C; YIL094C; YIL094C.
    GeneIDi854714.
    KEGGisce:YIL094C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z46728 Genomic DNA. Translation: CAA86700.1 .
    BK006942 Genomic DNA. Translation: DAA08459.1 .
    PIRi S49786.
    RefSeqi NP_012172.1. NM_001179442.1.

    3D structure databases

    ProteinModelPortali P40495.
    SMRi P40495. Positions 22-371.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34898. 68 interactions.
    DIPi DIP-4162N.
    IntActi P40495. 90 interactions.
    MINTi MINT-491742.
    STRINGi 4932.YIL094C.

    Chemistry

    BindingDBi P40495.
    ChEMBLi CHEMBL1075252.

    Proteomic databases

    MaxQBi P40495.
    PaxDbi P40495.
    PeptideAtlasi P40495.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YIL094C ; YIL094C ; YIL094C .
    GeneIDi 854714.
    KEGGi sce:YIL094C.

    Organism-specific databases

    CYGDi YIL094c.
    SGDi S000001356. LYS12.

    Phylogenomic databases

    eggNOGi COG0473.
    GeneTreei ENSGT00550000076087.
    HOGENOMi HOG000021111.
    KOi K05824.
    OMAi EFMGYPE.
    OrthoDBi EOG7R83BB.

    Enzyme and pathway databases

    UniPathwayi UPA00033 ; UER00030 .
    BioCyci YEAST:YIL094C-MONOMER.

    Miscellaneous databases

    NextBioi 977383.

    Gene expression databases

    Genevestigatori P40495.

    Family and domain databases

    Gene3Di 3.40.718.10. 1 hit.
    InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
    IPR001804. Isocitrate/isopropylmalate_DH.
    IPR024084. IsoPropMal-DH-like_dom.
    [Graphical view ]
    PANTHERi PTHR11835. PTHR11835. 1 hit.
    Pfami PF00180. Iso_dh. 1 hit.
    [Graphical view ]
    PROSITEi PS00470. IDH_IMDH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. Bienvenut W.V., Peters C.
      Submitted (JUN-2005) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 23-36; 103-114; 116-127; 181-192; 237-248; 309-318 AND 346-370, IDENTIFICATION BY MASS SPECTROMETRY.
    4. "Enzymatic formation of alpha-ketoadipic acid from homoisocitric acid."
      Strassman M., Ceci L.N.
      J. Biol. Chem. 240:4357-4361(1965) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    5. Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
    6. "General and specific controls of lysine biosynthesis in Saccharomyces cerevisiae."
      Urrestarazu L.A., Borell C.W., Bhattacharjee J.K.
      Curr. Genet. 9:341-344(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    7. "Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels."
      Shevchenko A., Jensen O.N., Podtelejnikov A.V., Sagliocco F., Wilm M., Vorm O., Mortensen P., Shevchenko A., Boucherie H., Mann M.
      Proc. Natl. Acad. Sci. U.S.A. 93:14440-14445(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
    8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
      Strain: ATCC 76625 / YPH499.
    11. "Complete kinetic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae."
      Lin Y., Alguindigue S.S., Volkman J., Nicholas K.M., West A.H., Cook P.F.
      Biochemistry 46:890-898(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION.
    12. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "Site-directed mutagenesis as a probe of the acid-base catalytic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae."
      Lin Y., West A.H., Cook P.F.
      Biochemistry 48:7305-7312(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF TYR-150 AND LYS-206.

    Entry informationi

    Entry nameiLYS12_YEAST
    AccessioniPrimary (citable) accession number: P40495
    Secondary accession number(s): D6VVJ3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 120 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 19079 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome IX
      Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

    External Data

    Dasty 3