ACEA_ORYSJ
ID ACEA_ORYSJ Reviewed; 572 AA.
AC Q6Z6M4; Q8W2F9;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Isocitrate lyase {ECO:0000303|PubMed:15944756};
DE Short=ICL {ECO:0000303|PubMed:15944756};
DE EC=4.1.3.1 {ECO:0000269|PubMed:15944756};
DE AltName: Full=Isocitrase {ECO:0000305};
DE AltName: Full=Isocitratase {ECO:0000305};
GN Name=ICL {ECO:0000303|PubMed:15944756};
GN OrderedLocusNames=Os07g0529000 {ECO:0000312|EMBL:BAF21753.1},
GN LOC_Os07g34520 {ECO:0000305};
GN ORFNames=OsJ_24528 {ECO:0000312|EMBL:EEE67304.1},
GN OSJNBa0007H12.39 {ECO:0000312|EMBL:BAC83656.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 499-572, TISSUE SPECIFICITY, AND INDUCTION BY
RP SENESCENCE.
RC STRAIN=cv. Tainung 67; TISSUE=Leaf;
RX PubMed=11432928; DOI=10.1093/jexbot/52.358.1117;
RA Lee R.-H., Wang C.-H., Huang L.-T., Chen S.-C.G.;
RT "Leaf senescence in rice plants: cloning and characterization of senescence
RT up-regulated genes.";
RL J. Exp. Bot. 52:1117-1121(2001).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, AND INDUCTION BY
RP SUBMERGENCE.
RX PubMed=15944756; DOI=10.1111/j.1745-7270.2005.00060.x;
RA Lu Y., Wu Y.R., Han B.;
RT "Anaerobic induction of isocitrate lyase and malate synthase in submerged
RT rice seedlings indicates the important metabolic role of the glyoxylate
RT cycle.";
RL Acta Biochim. Biophys. Sin. 37:406-414(2005).
RN [7]
RP INDUCTION BY SENESCENCE.
RX PubMed=23296688; DOI=10.1104/pp.112.205385;
RA Jan A., Maruyama K., Todaka D., Kidokoro S., Abo M., Yoshimura E.,
RA Shinozaki K., Nakashima K., Yamaguchi-Shinozaki K.;
RT "OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and
RT stress tolerance in rice by regulating stress-related genes.";
RL Plant Physiol. 161:1202-1216(2013).
CC -!- FUNCTION: Involved in storage lipid mobilization during the growth of
CC higher plant seedling. {ECO:0000269|PubMed:15944756}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-threo-isocitrate = glyoxylate + succinate;
CC Xref=Rhea:RHEA:13245, ChEBI:CHEBI:15562, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:36655; EC=4.1.3.1;
CC Evidence={ECO:0000269|PubMed:15944756};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P9WKK7};
CC -!- PATHWAY: Carbohydrate metabolism; glyoxylate cycle; (S)-malate from
CC isocitrate: step 1/2. {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Glyoxysome {ECO:0000269|PubMed:15944756}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves. {ECO:0000269|PubMed:11432928}.
CC -!- INDUCTION: By submergence in seedlings (PubMed:15944756). By dark-
CC induced senescence in leaves (PubMed:11432928, PubMed:23296688).
CC {ECO:0000269|PubMed:11432928, ECO:0000269|PubMed:15944756,
CC ECO:0000269|PubMed:23296688}.
CC -!- SIMILARITY: Belongs to the isocitrate lyase/PEP mutase superfamily.
CC Isocitrate lyase family. {ECO:0000305}.
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DR EMBL; AP004990; BAC83656.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF21753.1; -; Genomic_DNA.
DR EMBL; AP014963; BAT01864.1; -; Genomic_DNA.
DR EMBL; CM000144; EEE67304.1; -; Genomic_DNA.
DR EMBL; AF251075; AAL65398.1; -; mRNA.
DR RefSeq; XP_015644942.1; XM_015789456.1.
DR AlphaFoldDB; Q6Z6M4; -.
DR SMR; Q6Z6M4; -.
DR STRING; 4530.OS07T0529000-01; -.
DR PaxDb; Q6Z6M4; -.
DR PRIDE; Q6Z6M4; -.
DR EnsemblPlants; Os07t0529000-01; Os07t0529000-01; Os07g0529000.
DR GeneID; 4343441; -.
DR Gramene; Os07t0529000-01; Os07t0529000-01; Os07g0529000.
DR KEGG; osa:4343441; -.
DR eggNOG; KOG1260; Eukaryota.
DR HOGENOM; CLU_019214_2_2_1; -.
DR InParanoid; Q6Z6M4; -.
DR OMA; LEKDWAE; -.
DR OrthoDB; 905115at2759; -.
DR UniPathway; UPA00703; UER00719.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000007752; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR ExpressionAtlas; Q6Z6M4; baseline and differential.
DR Genevisible; Q6Z6M4; OS.
DR GO; GO:0009514; C:glyoxysome; IDA:UniProtKB.
DR GO; GO:0004451; F:isocitrate lyase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006097; P:glyoxylate cycle; NAS:UniProtKB.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
DR CDD; cd00377; ICL_PEPM; 1.
DR Gene3D; 3.20.20.60; -; 1.
DR InterPro; IPR039556; ICL/PEPM.
DR InterPro; IPR006254; Isocitrate_lyase.
DR InterPro; IPR018523; Isocitrate_lyase_ph_CS.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR PANTHER; PTHR21631; PTHR21631; 1.
DR Pfam; PF00463; ICL; 1.
DR PIRSF; PIRSF001362; Isocit_lyase; 1.
DR SUPFAM; SSF51621; SSF51621; 1.
DR TIGRFAMs; TIGR01346; isocit_lyase; 1.
DR PROSITE; PS00161; ISOCITRATE_LYASE; 1.
PE 1: Evidence at protein level;
KW Glyoxylate bypass; Glyoxysome; Lyase; Magnesium; Metal-binding; Peroxisome;
KW Reference proteome; Tricarboxylic acid cycle.
FT CHAIN 1..572
FT /note="Isocitrate lyase"
FT /id="PRO_0000430878"
FT REGION 550..572
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 570..572
FT /note="Microbody targeting signal"
FT /evidence="ECO:0000305"
FT COMPBIAS 553..572
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 213
FT /note="Proton acceptor"
FT /evidence="ECO:0000305"
FT BINDING 104..106
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WKK7"
FT BINDING 175
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P9WKK7"
FT BINDING 214..215
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WKK7"
FT BINDING 250
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WKK7"
FT BINDING 437..441
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WKK7"
FT BINDING 472
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P9WKK7"
SQ SEQUENCE 572 AA; 63051 MW; 38B141A2EEE76375 CRC64;
MSSPFSVPSL IMEEEGRFEA EVAEVEAWWG TDRFRLTKRP YTARDVALLR GTLRQSYASG
DMAKKLWRTL RAHQANGTAS RTFGALDPVQ VAMMAKHLDT VYVSGWQCSS THTSTNEPGP
DLADYPYDTV PNKVEHLFFA QLYHDRKQRE ARMSMSRAER AHEPYVDYLK PIIADGDTGF
GGATATVKLC KLFVERGAAG VHLEDQSSVT KKCGHMAGKV LVAVSEHVNR LVAARLQFDI
MGVETVLVAR TDAVAATLIQ TNVDARDHQF ILGATNPRLR NRSLAAVLSD AMSAGKNGRE
LQAIEDEWLA TAQLKTFSDC VRDAIASLNA TDADKQRKLQ EWSAATSHDK CVPLEQARDI
AAGLGVTSLF WDWDLPRTRE GFYRFRGSVA AAVVRGRAFA PHADVLWMET SSPNIAECTA
FAEGVRAASP GAMLAYNLSP SFNWDASGMT DADMSEFIPR VARLGYVWQF ITLAGFHADA
LVTDTFARDF ARRGMLAYVE RIQREERSNG VETLQHQKWS GANFYDRVLK TVQGGISSTA
AMGKGVTEEQ FKGSWTGPGS ESSSHVLAKS RM
