Isocitrate lyase - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P28240 (ACEA_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 119. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Isocitrate lyase
Short name=ICL
EC=4.1.3.1

Alternative name(s):
Threo-D(S)-isocitrate glyoxylate-lyase
Short name=Isocitrase
Short name=Isocitratase

Gene names

Name:	ICL1
Ordered Locus Names:	YER065C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	557 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	Isocitrate = succinate + glyoxylate.
Enzyme regulation	Phosphorylated and inactivated after addition of glucose to the cell culture (repressing conditions).
Pathway	Carbohydrate metabolism; glyoxylate cycle; (S)-malate from isocitrate: step 1/2.
Subunit structure	Homotetramer. Ref.7
Subcellular location	Cytoplasm Ref.8 Ref.11.
Induction	Repressed by glucose and induced by ethanol via the transcriptional activator CAT8. Ref.2 Ref.6 Ref.12
Post-translational modification	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). Ref.6
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.
Sequence similarities	Belongs to the isocitrate lyase/PEP mutase superfamily. Isocitrate lyase family.
Biophysicochemical properties	Kinetic parameters: The Vmax with threo-D(S)-isocitrate as substrate is 5-fold higher than with threo-D(S)-2-methylisocitrate as substrate. K_M=1.4 mM for threo-D(S)-isocitrate (at pH 7.0) Ref.5 Ref.7 K_M=0.6 mM for threo-D(S)-2-methylisocitrate (at pH 7.0 and 30 degrees Celsius) pH dependence: Optimum pH is 7. Temperature dependence: Thermostable for 60 minutes up to 50 degrees Celsius.

Ontologies

Keywords
Biological process	Glyoxylate bypass Tricarboxylic acid cycle
Cellular component	Cytoplasm
Molecular function	Lyase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	glyoxylate cycle Traceable author statement PubMed 11092862. Source: SGD tricarboxylic acid cycle Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	isocitrate lyase activity Inferred from mutant phenotype Ref.1. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 557

557

Isocitrate lyase

PRO_0000068799

Sites

Active site

217

Probable

Amino acid modifications

Modified residue

Phosphothreonine Potential

Experimental info

Mutagenesis

T → A: Abolishes short-term enzyme inactivation by glucose addition. Ref.9

Mutagenesis

216

K → R: Reduces activity by 45%; when associated with L-220. Ref.10

Mutagenesis

220

M → L: Reduces activity by 45%; when associated with R-216. Ref.10

Sequences

Sequence

Length

Mass (Da)

Tools

P28240 [UniParc].

Last modified December 1, 1992. Version 1.
Checksum: 15CC5A169CCEBE8B
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FASTA

557

62,409

        10         20         30         40         50         60 
MPIPVGNTKN DFAALQAKLD ADAAEIEKWW SDSRWSKTKR NYSARDIAVR RGTFPPIEYP 

        70         80         90        100        110        120 
SSVMARKLFK VLEKHHNEGT VSKTFGALDP VQISQMAKYL DTIYISGWQC SSTASTSNEP 

       130        140        150        160        170        180 
GPDLADYPMD TVPNKVEHLF KAQLFHDRKQ LEARSKAKSQ EELDEMGAPI DYLTPIVADA 

       190        200        210        220        230        240 
DAGHGGLTAV FKLTKMFIER GAAGIHMEDQ TSTNKKCGHM AGRCVIPVQE HVNRLVTIRM 

       250        260        270        280        290        300 
CADIMHSDLI VVARTDSEAA TLISSTIDTR DHYFIVGATN PNIEPFAEVL NDAIMSGASG 

       310        320        330        340        350        360 
QELADIEQKW CRDAGLKLFH EAVIDEIERS ALSNKQELIK KFTSKVGPLT ETSHREAKKL 

       370        380        390        400        410        420 
AKEILGHEIF FDWELPRVRE GLYRYRGGTQ CSIMRARAFA PYADLVWMES NYPDFQQAKE 

       430        440        450        460        470        480 
FAEGVKEKFP DQWLAYNLSP SFNWPKAMSV DEQHTFIQRL GDLGYIWQFI TLAGLHTNAL 

       490        500        510        520        530        540 
AVHNFSRDFA KDGMKAYAQN VQQREMDDGV DVLKHQKWSG AEYIDGLLKL AQGGVSATAA 

       550 
MGTGVTEDQF KENGVKK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The ICL1 gene from Saccharomyces cerevisiae." Fernandez E., Moreno F., Rodicio R. Eur. J. Biochem. 204:983-990(1992) [PubMed] [Europe PMC] [Abstract] 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]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X61271 Genomic DNA. Translation: CAA43575.1. X65554 Genomic DNA. Translation: CAA46523.1. U18813 Genomic DNA. Translation: AAB64601.1. BK006939 Genomic DNA. Translation: DAA07724.1.
PIR	WZBYI. S22386.
RefSeq	NP_010987.3. NM_001178956.3.
3D structure databases
ProteinModelPortal	P28240.
SMR	P28240. Positions 22-534.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1663N.
IntAct	P28240. 2 interactions.
MINT	MINT-400647.
STRING	4932.YER065C.
Proteomic databases
PaxDb	P28240.
PeptideAtlas	P28240.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YER065C; YER065C; YER065C.
GeneID	856794.
KEGG	sce:YER065C. sce:YER068W.
Organism-specific databases
CYGD	YER065c.
SGD	S000000867. ICL1.
Phylogenomic databases
eggNOG	COG2224.
GeneTree	ENSGT00510000053163.
HOGENOM	HOG000238475.
KO	K01637. K10643.
OMA	MVTQMAK.
OrthoDB	EOG4P5PJP.
Enzyme and pathway databases
SABIO-RK	P28240.
UniPathway	UPA00703; UER00719.
Gene expression databases
Genevestigator	P28240.
GermOnline	YER065C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.20.20.60. 2 hits.
InterPro	IPR006254. Isocitrate_lyase. IPR000918. Isocitrate_lyase/Pmutase. IPR018523. Isocitrate_lyase_ph_CS. IPR015813. Pyrv/PenolPyrv_Kinase. [Graphical view]
PANTHER	PTHR21631:SF3. PTHR21631:SF3. 1 hit.
Pfam	PF00463. ICL. 1 hit. [Graphical view]
PIRSF	PIRSF001362. Isocit_lyase. 1 hit.
SUPFAM	SSF51621. Pyrv/PenolPyrv_Kinase_cat. 1 hit.
TIGRFAMs	TIGR01346. isocit_lyase. 1 hit.
PROSITE	PS00161. ISOCITRATE_LYASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	983030.

Entry information

Entry name

ACEA_YEAST

Accession

Primary (citable) accession number: P28240
Secondary accession number(s): D3DLX0

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	December 1, 1992
Last modified:	May 1, 2013
This is version 119 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome V

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents