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P40495

- LYS12_YEAST

UniProt

P40495 - LYS12_YEAST

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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

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
Complete GO annotation...

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-KW
Complete GO annotation...

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. 69 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.
InParanoidiP40495.
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

        10         20         30         40         50
MFRSVATRLS ACRGLASNAA RKSLTIGLIP GDGIGKEVIP AGKQVLENLN
60 70 80 90 100
SKHGLSFNFI DLYAGFQTFQ ETGKALPDET VKVLKEQCQG ALFGAVQSPT
110 120 130 140 150
TKVEGYSSPI VALRREMGLF ANVRPVKSVE GEKGKPIDMV IVRENTEDLY
160 170 180 190 200
IKIEKTYIDK ATGTRVADAT KRISEIATRR IATIALDIAL KRLQTRGQAT
210 220 230 240 250
LTVTHKSNVL SQSDGLFREI CKEVYESNKD KYGQIKYNEQ IVDSMVYRLF
260 270 280 290 300
REPQCFDVIV APNLYGDILS DGAAALVGSL GVVPSANVGP EIVIGEPCHG
310 320 330 340 350
SAPDIAGKGI ANPIATIRST ALMLEFLGHN EAAQDIYKAV DANLREGSIK
360 370
TPDLGGKAST QQVVDDVLSR L
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. 69 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.
InParanoidi P40495.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 121 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