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Protein

Isocitrate lyase

Gene

ICL1

Organism
Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

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.By similarity

Catalytic activityi

Isocitrate = succinate + glyoxylate.By similarity
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.By similarity

Cofactori

Mg2+By similarity

Pathway: glyoxylate cycle

This protein is involved in step 1 of the subpathway that synthesizes (S)-malate from isocitrate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Isocitrate lyase (ICL1)
  2. Malate synthase (YALI0_D19140g), Malate synthase (YALI0_E15708g)
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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi165 – 1651MagnesiumBy similarity
Active sitei203 – 2031Proton acceptorBy similarity
Binding sitei240 – 2401SubstrateBy similarity
Binding sitei457 – 4571SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00703; UER00719.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate lyase1 Publication (EC:4.1.3.1By similarity)
Short name:
ICLCurated
Short name:
IsocitraseCurated
Short name:
IsocitrataseCurated
Alternative name(s):
Methylisocitrate lyaseBy similarity (EC:4.1.3.30By similarity)
Short name:
MICACurated
Threo-D(S)-isocitrate glyoxylate-lyaseCurated
Gene namesi
Name:ICL11 Publication
Ordered Locus Names:YALI0C16885g
OrganismiYarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
Taxonomic identifieri284591 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesDipodascaceaeYarrowia
ProteomesiUP000001300 Componenti: Chromosome C

Subcellular locationi

  • Glyoxysome By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Glyoxysome, Peroxisome

Pathology & Biotechi

Disruption phenotypei

Inhibits the utilization of acetate, ethanol, and fatty acids, but also reduces the growth rate on glucose.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 540540Isocitrate lyasePRO_0000068798Add
BLAST

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi4952.XP_501923.1.

Structurei

3D structure databases

ProteinModelPortaliP41555.
SMRiP41555. Positions 3-520.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni93 – 953Substrate bindingBy similarity
Regioni204 – 2052Substrate bindingBy similarity
Regioni423 – 4275Substrate bindingBy similarity

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi538 – 5403Microbody targeting signalSequence Analysis

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG2224.
HOGENOMiHOG000238475.
InParanoidiP41555.
KOiK01637.
OMAiDAIHKEY.
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]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR01346. isocit_lyase. 1 hit.
PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P41555-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEQQRFNNE VEEIKKWWSS PRWKHTKRVY SPEDIASRRG TIKVPQASSQ
60 70 80 90 100
QADKLFKLLQ EHEKNHTASF TYGALDPVQV TQMAKYLDSI YVSGWQSSST
110 120 130 140 150
ASTSNEPSPD LADYPMDTVP NKVEHLWFAQ LFHDRKQNEE RLSLPESERS
160 170 180 190 200
KLPAPVDYLR PIIADADTGH GGLTAVVKLT KMFIERGAAG IHIEDQAPGT
210 220 230 240 250
KKCGHMAGKV LVPIQEHINR LIAIRASADI FGSDLLAIAR TDSEAATLIT
260 270 280 290 300
SSIDYRDHYF IAGATNKDAG HLVDVMVAAE LEGKQGAALQ AVEDEWNRKA
310 320 330 340 350
GVKLFHEAFA DEVNAGSYSN KAELIAEFNK KVTPLSNTPA LEARALAARL
360 370 380 390 400
LGKDIYFNWE AARVREGYYR YQGGTQCAVN RGIAYAPYAD LIWMESKLPD
410 420 430 440 450
YAQAKEFAEG VKNAVPHQWL AYNLSPSFNW TTAMSPEDQE TYISRLAKLG
460 470 480 490 500
YVWQFITLAG LHTNALISDK FAKAYSERGM KAYGGEIQQP EIDQGCEVVK
510 520 530 540
HQKWSGAEYI DGILRMVTGG ITSTAAMGAG VTEDQFKSKL
Length:540
Mass (Da):60,049
Last modified:October 11, 2004 - v3
Checksum:i340B608321946098
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti73 – 742GA → AS in CAA51362 (PubMed:8246896).Curated
Sequence conflicti97 – 971S → C in CAA51362 (PubMed:8246896).Curated
Sequence conflicti107 – 1071P → S in CAA51362 (PubMed:8246896).Curated
Sequence conflicti112 – 1132AD → GG in CAA51362 (PubMed:8246896).Curated
Sequence conflicti134 – 1341D → E in CAA51362 (PubMed:8246896).Curated
Sequence conflicti149 – 1557RSKLPAP → PIQAPRAR in CAA51362 (PubMed:8246896).Curated
Sequence conflicti167 – 1671D → E in CAA51362 (PubMed:8246896).Curated
Sequence conflicti232 – 2343GSD → ALN in CAA51362 (PubMed:8246896).Curated
Sequence conflicti281 – 2888LEGKQGAA → ARGQAGAP in CAA51362 (PubMed:8246896).Curated
Sequence conflicti315 – 3151A → D in CAA51362 (PubMed:8246896).Curated
Sequence conflicti340 – 3456ALEARA → DIEDRY in CAA51362 (PubMed:8246896).Curated
Sequence conflicti383 – 3842IA → YS in CAA51362 (PubMed:8246896).Curated
Sequence conflicti471 – 4722FA → SC in CAA51362 (PubMed:8246896).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X72848 Genomic DNA. Translation: CAA51362.1.
CR382129 Genomic DNA. Translation: CAG82243.1.
RefSeqiXP_501923.1. XM_501923.1.

Genome annotation databases

EnsemblFungiiCAG82243; CAG82243; YALI0_C16885g.
GeneIDi2909302.
KEGGiyli:YALI0C16885g.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X72848 Genomic DNA. Translation: CAA51362.1.
CR382129 Genomic DNA. Translation: CAG82243.1.
RefSeqiXP_501923.1. XM_501923.1.

3D structure databases

ProteinModelPortaliP41555.
SMRiP41555. Positions 3-520.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi4952.XP_501923.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAG82243; CAG82243; YALI0_C16885g.
GeneIDi2909302.
KEGGiyli:YALI0C16885g.

Phylogenomic databases

eggNOGiCOG2224.
HOGENOMiHOG000238475.
InParanoidiP41555.
KOiK01637.
OMAiDAIHKEY.
OrthoDBiEOG73Z331.

Enzyme and pathway databases

UniPathwayiUPA00703; UER00719.

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]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR01346. isocit_lyase. 1 hit.
PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning of the isocitrate lyase gene (ICL1) from Yarrowia lipolytica and characterization of the deduced protein."
    Barth G., Scheuber T.
    Mol. Gen. Genet. 241:422-430(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DISRUPTION PHENOTYPE.
    Strain: B204-12C.
  2. Juretzek T.
    Submitted (DEC-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "Genome evolution in yeasts."
    Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., Lafontaine I., de Montigny J., Marck C., Neuveglise C., Talla E., Goffard N., Frangeul L., Aigle M., Anthouard V., Babour A., Barbe V., Barnay S., Blanchin S.
    , Beckerich J.-M., Beyne E., Bleykasten C., Boisrame A., Boyer J., Cattolico L., Confanioleri F., de Daruvar A., Despons L., Fabre E., Fairhead C., Ferry-Dumazet H., Groppi A., Hantraye F., Hennequin C., Jauniaux N., Joyet P., Kachouri R., Kerrest A., Koszul R., Lemaire M., Lesur I., Ma L., Muller H., Nicaud J.-M., Nikolski M., Oztas S., Ozier-Kalogeropoulos O., Pellenz S., Potier S., Richard G.-F., Straub M.-L., Suleau A., Swennen D., Tekaia F., Wesolowski-Louvel M., Westhof E., Wirth B., Zeniou-Meyer M., Zivanovic Y., Bolotin-Fukuhara M., Thierry A., Bouchier C., Caudron B., Scarpelli C., Gaillardin C., Weissenbach J., Wincker P., Souciet J.-L.
    Nature 430:35-44(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CLIB 122 / E 150.

Entry informationi

Entry nameiACEA_YARLI
AccessioniPrimary (citable) accession number: P41555
Secondary accession number(s): Q6CBN9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: October 11, 2004
Last modified: June 24, 2015
This is version 102 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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.