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Protein

Isocitrate lyase

Gene

ICL1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the 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. Required for growth on ethanol or acetate, but dispensable when fermentable carbon sources are available. Acts also on 2-methylisocitrate.

Catalytic activityi

Isocitrate = succinate + glyoxylate.PROSITE-ProRule annotation

Enzyme regulationi

Phosphorylated and inactivated after addition of glucose to the cell culture (repressing conditions).

Kineticsi

The Vmax with threo-D(S)-isocitrate as substrate is 5-fold higher than with threo-D(S)-2-methylisocitrate as substrate.

  1. KM=1.4 mM for threo-D(S)-isocitrate (at pH 7.0)2 Publications
  2. KM=0.6 mM for threo-D(S)-2-methylisocitrate (at pH 7.0 and 30 degrees Celsius)2 Publications

pH dependencei

Optimum pH is 7.2 Publications

Temperature dependencei

Thermostable for 60 minutes up to 50 degrees Celsius.2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei217 – 2171Curated

GO - Molecular functioni

  1. isocitrate lyase activity Source: SGD

GO - Biological processi

  1. glyoxylate cycle Source: SGD
  2. tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Enzyme and pathway databases

BioCyciYEAST:YER065C-MONOMER.
SABIO-RKP28240.
UniPathwayiUPA00703; UER00719.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate lyase (EC:4.1.3.1)
Short name:
ICL
Alternative name(s):
Threo-D(S)-isocitrate glyoxylate-lyase
Short name:
Isocitrase
Short name:
Isocitratase
Gene namesi
Name:ICL1
Ordered Locus Names:YER065C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome V

Organism-specific databases

CYGDiYER065c.
SGDiS000000867. ICL1.

Subcellular locationi

Cytoplasm 2 Publications

GO - Cellular componenti

  1. cytoplasm Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi53 – 531T → A: Abolishes short-term enzyme inactivation by glucose addition. 1 Publication
Mutagenesisi216 – 2161K → R: Reduces activity by 45%; when associated with L-220. 1 Publication
Mutagenesisi220 – 2201M → L: Reduces activity by 45%; when associated with R-216. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 557557Isocitrate lyasePRO_0000068799Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei53 – 531PhosphothreonineSequence Analysis

Post-translational modificationi

Phosphorylated in response to elevated glucose levels, leading first to reversible inactivation of the enzyme (short-term inactivation), and at a later stage to proteolytic degradation of the protein (long-term inactivation).1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP28240.
PaxDbiP28240.
PeptideAtlasiP28240.

Expressioni

Inductioni

Repressed by glucose and induced by ethanol via the transcriptional activator CAT8.3 Publications

Gene expression databases

GenevestigatoriP28240.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi36807. 30 interactions.
DIPiDIP-1663N.
IntActiP28240. 2 interactions.
MINTiMINT-400647.
STRINGi4932.YER065C.

Structurei

3D structure databases

ProteinModelPortaliP28240.
SMRiP28240. Positions 22-534.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG2224.
GeneTreeiENSGT00510000053163.
HOGENOMiHOG000238475.
InParanoidiP28240.
KOiK01637.
OMAiEMEQGVD.
OrthoDBiEOG73Z331.

Family and domain databases

Gene3Di3.20.20.60. 2 hits.
InterProiIPR006254. Isocitrate_lyase.
IPR018523. Isocitrate_lyase_ph_CS.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PANTHERiPTHR21631:SF3. PTHR21631:SF3. 1 hit.
PfamiPF00463. ICL. 1 hit.
[Graphical view]
PIRSFiPIRSF001362. Isocit_lyase. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR01346. isocit_lyase. 1 hit.
PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P28240-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPIPVGNTKN DFAALQAKLD ADAAEIEKWW SDSRWSKTKR NYSARDIAVR
60 70 80 90 100
RGTFPPIEYP SSVMARKLFK VLEKHHNEGT VSKTFGALDP VQISQMAKYL
110 120 130 140 150
DTIYISGWQC SSTASTSNEP GPDLADYPMD TVPNKVEHLF KAQLFHDRKQ
160 170 180 190 200
LEARSKAKSQ EELDEMGAPI DYLTPIVADA DAGHGGLTAV FKLTKMFIER
210 220 230 240 250
GAAGIHMEDQ TSTNKKCGHM AGRCVIPVQE HVNRLVTIRM CADIMHSDLI
260 270 280 290 300
VVARTDSEAA TLISSTIDTR DHYFIVGATN PNIEPFAEVL NDAIMSGASG
310 320 330 340 350
QELADIEQKW CRDAGLKLFH EAVIDEIERS ALSNKQELIK KFTSKVGPLT
360 370 380 390 400
ETSHREAKKL AKEILGHEIF FDWELPRVRE GLYRYRGGTQ CSIMRARAFA
410 420 430 440 450
PYADLVWMES NYPDFQQAKE FAEGVKEKFP DQWLAYNLSP SFNWPKAMSV
460 470 480 490 500
DEQHTFIQRL GDLGYIWQFI TLAGLHTNAL AVHNFSRDFA KDGMKAYAQN
510 520 530 540 550
VQQREMDDGV DVLKHQKWSG AEYIDGLLKL AQGGVSATAA MGTGVTEDQF

KENGVKK
Length:557
Mass (Da):62,409
Last modified:December 1, 1992 - v1
Checksum:i15CC5A169CCEBE8B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X61271 Genomic DNA. Translation: CAA43575.1.
X65554 Genomic DNA. Translation: CAA46523.1.
U18813 Genomic DNA. Translation: AAB64601.1.
BK006939 Genomic DNA. Translation: DAA07724.1.
PIRiS22386. WZBYI.
RefSeqiNP_010987.3. NM_001178956.3.

Genome annotation databases

EnsemblFungiiYER065C; YER065C; YER065C.
GeneIDi856794.
KEGGisce:YER065C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X61271 Genomic DNA. Translation: CAA43575.1.
X65554 Genomic DNA. Translation: CAA46523.1.
U18813 Genomic DNA. Translation: AAB64601.1.
BK006939 Genomic DNA. Translation: DAA07724.1.
PIRiS22386. WZBYI.
RefSeqiNP_010987.3. NM_001178956.3.

3D structure databases

ProteinModelPortaliP28240.
SMRiP28240. Positions 22-534.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36807. 30 interactions.
DIPiDIP-1663N.
IntActiP28240. 2 interactions.
MINTiMINT-400647.
STRINGi4932.YER065C.

Proteomic databases

MaxQBiP28240.
PaxDbiP28240.
PeptideAtlasiP28240.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER065C; YER065C; YER065C.
GeneIDi856794.
KEGGisce:YER065C.

Organism-specific databases

CYGDiYER065c.
SGDiS000000867. ICL1.

Phylogenomic databases

eggNOGiCOG2224.
GeneTreeiENSGT00510000053163.
HOGENOMiHOG000238475.
InParanoidiP28240.
KOiK01637.
OMAiEMEQGVD.
OrthoDBiEOG73Z331.

Enzyme and pathway databases

UniPathwayiUPA00703; UER00719.
BioCyciYEAST:YER065C-MONOMER.
SABIO-RKP28240.

Miscellaneous databases

NextBioi983030.

Gene expression databases

GenevestigatoriP28240.

Family and domain databases

Gene3Di3.20.20.60. 2 hits.
InterProiIPR006254. Isocitrate_lyase.
IPR018523. Isocitrate_lyase_ph_CS.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PANTHERiPTHR21631:SF3. PTHR21631:SF3. 1 hit.
PfamiPF00463. ICL. 1 hit.
[Graphical view]
PIRSFiPIRSF001362. Isocit_lyase. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR01346. isocit_lyase. 1 hit.
PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Structure and regulation of the isocitrate lyase gene ICL1 from the yeast Saccharomyces cerevisiae."
    Schoeler A., Schueller H.-J.
    Curr. Genet. 23:375-381(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
    Strain: DBY939.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Production of pyruvate and succinate by action of isocitrate lyase on alpha-methylisocitrate."
    McFadden B.A., Rose I.A., Williams J.O.
    Arch. Biochem. Biophys. 148:84-88(1972) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, BIOPHYSICOCHEMICAL PROPERTIES.
  6. "Glucose-stimulated phosphorylation of yeast isocitrate lyase in vivo."
    Lopez-Boado Y.S., Herrero P., Fernandez M.-T., Fernandez R., Moreno F.
    J. Gen. Microbiol. 134:2499-2505(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION, INDUCTION.
  7. "Purification of isocitrate lyase from Saccharomyces cerevisiae."
    Lopez-Boado Y.S., Herrero P., Fernandez M.-T., Fernandez R., Moreno F.
    Yeast 4:41-46(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
  8. "Localization and targeting of isocitrate lyases in Saccharomyces cerevisiae."
    Taylor K.M., Kaplan C.P., Gao X., Baker A.
    Biochem. J. 319:255-262(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  9. "Glucose-induced inactivation of isocitrate lyase in Saccharomyces cerevisiae is mediated by the cAMP-dependent protein kinase catalytic subunits Tpk1 and Tpk2."
    Ordiz I., Herrero P., Rodicio R., Moreno F.
    FEBS Lett. 385:43-46(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF THR-53.
  10. "Molecular genetics of ICL2, encoding a non-functional isocitrate lyase in Saccharomyces cerevisiae."
    Heinisch J.J., Valdes E., Alvarez J., Rodicio R.
    Yeast 12:1285-1295(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LYS-216 AND MET-220.
  11. "Isocitrate lyase localisation in Saccharomyces cerevisiae cells."
    Chaves R.S., Herrero P., Ordiz I., Angeles del Brio M., Moreno F.
    Gene 198:165-169(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  12. "Deregulation of gluconeogenic structural genes by variants of the transcriptional activator Cat8p of the yeast Saccharomyces cerevisiae."
    Rahner A., Hiesinger M., Schueller H.-J.
    Mol. Microbiol. 34:146-156(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.

Entry informationi

Entry nameiACEA_YEAST
AccessioniPrimary (citable) accession number: P28240
Secondary accession number(s): D3DLX0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: January 7, 2015
This is version 130 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Yeast isocitrate lyase is the only eukaryotic member of this family that is located in the cytoplasm, instead of being targeted to the peroxisome or the glyoxysome.
The Pseudomonas indigofera ortholog enzyme can be inactivated by beta-bromopyruvate.

Keywords - Technical termi

Complete proteome, 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 V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

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.