LEUC_ARATH
ID LEUC_ARATH Reviewed; 509 AA.
AC Q94AR8; Q9T0L4;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=3-isopropylmalate dehydratase large subunit, chloroplastic {ECO:0000305};
DE EC=4.2.1.33 {ECO:0000269|PubMed:19597944};
DE AltName: Full=2-(omega-methylthio)alkylmalate dehydratase large subunit {ECO:0000305};
DE EC=4.2.1.170 {ECO:0000269|PubMed:19597944};
DE AltName: Full=AtLEUC {ECO:0000303|PubMed:20663849};
DE AltName: Full=Isopropylmalate isomerase large subunit 1 {ECO:0000303|PubMed:19150812, ECO:0000303|PubMed:19597944};
DE Short=AtIIL1 {ECO:0000303|PubMed:19150812};
DE Short=IPMI LSU1 {ECO:0000303|PubMed:19597944};
DE AltName: Full=Methylthioalkylmalate isomerase large subunit {ECO:0000305};
DE Short=MAM-IL {ECO:0000305};
DE Flags: Precursor;
GN Name=IIL1 {ECO:0000303|PubMed:19150812};
GN OrderedLocusNames=At4g13430 {ECO:0000312|Araport:AT4G13430};
GN ORFNames=T9E8.170 {ECO:0000312|EMBL:CAB40778.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=cv. Bur-0, cv. Columbia, and cv. Pf-0;
RX PubMed=19150812; DOI=10.1126/science.1164014;
RA Sureshkumar S., Todesco M., Schneeberger K., Harilal R.,
RA Balasubramanian S., Weigel D.;
RT "A genetic defect caused by a triplet repeat expansion in Arabidopsis
RT thaliana.";
RL Science 323:1060-1063(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [6]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=19597944; DOI=10.1007/s11103-009-9519-5;
RA Knill T., Reichelt M., Paetz C., Gershenzon J., Binder S.;
RT "Arabidopsis thaliana encodes a bacterial-type heterodimeric
RT isopropylmalate isomerase involved in both Leu biosynthesis and the Met
RT chain elongation pathway of glucosinolate formation.";
RL Plant Mol. Biol. 71:227-239(2009).
RN [7]
RP FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=20663849; DOI=10.1093/pcp/pcq113;
RA He Y., Chen B., Pang Q., Strul J.M., Chen S.;
RT "Functional specification of Arabidopsis isopropylmalate isomerases in
RT glucosinolate and leucine biosynthesis.";
RL Plant Cell Physiol. 51:1480-1487(2010).
CC -!- FUNCTION: Catalyzes the isomerization between 2-isopropylmalate and 3-
CC isopropylmalate, via the formation of 2-isopropylmaleate
CC (PubMed:19150812, PubMed:20663849). Functions in both the biosynthesis
CC of leucine and in the methionine chain elongation pathway of aliphatic
CC glucosinolate formation (PubMed:19597944).
CC {ECO:0000269|PubMed:19150812, ECO:0000269|PubMed:19597944,
CC ECO:0000269|PubMed:20663849}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate;
CC Xref=Rhea:RHEA:32287, ChEBI:CHEBI:1178, ChEBI:CHEBI:35121;
CC EC=4.2.1.33; Evidence={ECO:0000269|PubMed:19597944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2-(omega-methylsulfanyl)alkylmalate = a 2-(omega-
CC methylsulfanyl)alkylmaleate + H2O; Xref=Rhea:RHEA:50632, Rhea:RHEA-
CC COMP:12824, Rhea:RHEA-COMP:12826, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:133494, ChEBI:CHEBI:133498; EC=4.2.1.170;
CC Evidence={ECO:0000269|PubMed:19597944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-(3-methylsulfanyl)propylmalate = 2-(2-
CC methylsulfanyl)propylmaleate + H2O; Xref=Rhea:RHEA:50652,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:58817, ChEBI:CHEBI:133500;
CC EC=4.2.1.170; Evidence={ECO:0000269|PubMed:19597944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3-(omega-methylsulfanyl)alkylmalate = a 2-(omega-
CC methylsulfanyl)alkylmaleate + H2O; Xref=Rhea:RHEA:50636, Rhea:RHEA-
CC COMP:12825, Rhea:RHEA-COMP:12826, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:133496, ChEBI:CHEBI:133498; EC=4.2.1.170;
CC Evidence={ECO:0000269|PubMed:19597944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-(2-methylsulfanyl)ethylmalate = 2-(2-
CC methylsulfanyl)ethylmaleate + H2O; Xref=Rhea:RHEA:50648,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:58816, ChEBI:CHEBI:133499;
CC EC=4.2.1.170; Evidence={ECO:0000269|PubMed:19597944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-(2-methylsulfanyl)ethylmalate = 2-(2-
CC methylsulfanyl)ethylmaleate + H2O; Xref=Rhea:RHEA:50656,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:133497, ChEBI:CHEBI:133499;
CC EC=4.2.1.170; Evidence={ECO:0000269|PubMed:19597944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-(3-methylsulfanyl)propylmalate = 2-(2-
CC methylsulfanyl)propylmaleate + H2O; Xref=Rhea:RHEA:50660,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:133500, ChEBI:CHEBI:133501;
CC EC=4.2.1.170; Evidence={ECO:0000269|PubMed:19597944};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:P16276};
CC Note=Binds 1 [4Fe-4S] cluster per subunit.
CC {ECO:0000250|UniProtKB:P16276};
CC -!- PATHWAY: Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine
CC from 3-methyl-2-oxobutanoate: step 2/4. {ECO:0000305}.
CC -!- SUBUNIT: Heterodimer of the large LEUC/IIL1 subunit and the small LEUD
CC (SSU1, SSU2 or SSU3) subunits. {ECO:0000269|PubMed:20663849}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:18431481, ECO:0000269|PubMed:20663849}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers.
CC Expressed at low levels in siliques. {ECO:0000269|PubMed:20663849}.
CC -!- MISCELLANEOUS: The environment dependent reduction in IIL1 activity and
CC severely impaired growth of cv. Bur-0 are caused by a triplet repeat
CC expansion in the third intron of the gene (PubMed:19150812).
CC {ECO:0000305|PubMed:19150812}.
CC -!- SIMILARITY: Belongs to the aconitase/IPM isomerase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB40778.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78385.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL049608; CAB40778.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161536; CAB78385.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83278.1; -; Genomic_DNA.
DR EMBL; AY045842; AAK76516.1; -; mRNA.
DR EMBL; AY117151; AAM51226.1; -; mRNA.
DR PIR; T06300; T06300.
DR RefSeq; NP_567405.1; NM_117417.4.
DR AlphaFoldDB; Q94AR8; -.
DR SMR; Q94AR8; -.
DR BioGRID; 12272; 8.
DR STRING; 3702.AT4G13430.1; -.
DR iPTMnet; Q94AR8; -.
DR PaxDb; Q94AR8; -.
DR PRIDE; Q94AR8; -.
DR ProteomicsDB; 250756; -.
DR EnsemblPlants; AT4G13430.1; AT4G13430.1; AT4G13430.
DR GeneID; 826975; -.
DR Gramene; AT4G13430.1; AT4G13430.1; AT4G13430.
DR KEGG; ath:AT4G13430; -.
DR Araport; AT4G13430; -.
DR TAIR; locus:2142120; AT4G13430.
DR eggNOG; KOG0454; Eukaryota.
DR HOGENOM; CLU_006714_3_4_1; -.
DR InParanoid; Q94AR8; -.
DR OMA; CNMSIEM; -.
DR OrthoDB; 265826at2759; -.
DR PhylomeDB; Q94AR8; -.
DR BioCyc; ARA:AT4G13430-MON; -.
DR BioCyc; MetaCyc:AT4G13430-MON; -.
DR BRENDA; 4.2.1.170; 399.
DR BRENDA; 4.2.1.33; 399.
DR UniPathway; UPA00048; UER00071.
DR PRO; PR:Q94AR8; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94AR8; baseline and differential.
DR Genevisible; Q94AR8; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0003861; F:3-isopropylmalate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0050486; F:intramolecular transferase activity, transferring hydroxy groups; IMP:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019761; P:glucosinolate biosynthetic process; IMP:TAIR.
DR GO; GO:0009098; P:leucine biosynthetic process; IEA:UniProtKB-UniPathway.
DR CDD; cd01583; IPMI; 1.
DR Gene3D; 3.30.499.10; -; 2.
DR InterPro; IPR015931; Acnase/IPM_dHydase_lsu_aba_1/3.
DR InterPro; IPR001030; Acoase/IPM_deHydtase_lsu_aba.
DR InterPro; IPR036008; Aconitase_4Fe-4S_dom.
DR InterPro; IPR006251; Homoacnase/IPMdehydase_lsu.
DR InterPro; IPR033941; IPMI_cat.
DR Pfam; PF00330; Aconitase; 1.
DR PRINTS; PR00415; ACONITASE.
DR SUPFAM; SSF53732; SSF53732; 1.
DR TIGRFAMs; TIGR01343; hacA_fam; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Amino-acid biosynthesis; Branched-chain amino acid biosynthesis;
KW Chloroplast; Iron; Iron-sulfur; Leucine biosynthesis; Lyase; Metal-binding;
KW Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..47
FT /note="Chloroplast"
FT /evidence="ECO:0000305"
FT CHAIN 48..509
FT /note="3-isopropylmalate dehydratase large subunit,
FT chloroplastic"
FT /id="PRO_0000366939"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 376
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P16276"
FT BINDING 445
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P16276"
FT BINDING 448
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P16276"
SQ SEQUENCE 509 AA; 55014 MW; 6CE200D838894ECC CRC64;
MASVISSSPF LCKSSSKSDL GISSFPKSSQ ISIHRCQKKS ISRKIVSVMA PQKDRSPGTT
GSVKTGMTMT EKILARASEK SLVVPGDNIW VNVDVLMTHD VCGPGAFGIF KREFGEKAKV
WDPEKIVVIP DHYIFTADKR ANRNVDIMRE HCREQNIKYF YDITDLGNFK ANPDYKGVCH
VALAQEGHCR PGEVLLGTDS HTCTAGAFGQ FATGIGNTDA GFVLGTGKIL LKVPPTMRFI
LDGEMPSYLQ AKDLILQIIG EISVAGATYK TMEFSGTTIE SLSMEERMTL CNMVVEAGGK
NGVIPPDATT LNYVENRTSV PFEPVYSDGN ASFVADYRFD VSKLEPVVAK PHSPDNRALA
RECKDVKIDR VYIGSCTGGK TEDFMAAAKL FHAAGRKVKV PTFLVPATQK VWMDVYALPV
PGAGGKTCAQ IFEEAGCDTP ASPSCGACLG GPADTYARLN EPQVCVSTTN RNFPGRMGHK
EGQIYLASPY TAAASALTGR VADPREFLQ
