ILVD_ARATH
ID ILVD_ARATH Reviewed; 608 AA.
AC Q9LIR4; F4J5B4; Q94BS6;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Dihydroxy-acid dehydratase, chloroplastic {ECO:0000303|PubMed:29995859};
DE Short=AthDHAD {ECO:0000303|PubMed:29995859};
DE Short=DAD;
DE EC=4.2.1.9 {ECO:0000269|PubMed:29995859};
DE Flags: Precursor;
GN Name=DHAD {ECO:0000305};
GN OrderedLocusNames=At3g23940 {ECO:0000312|Araport:AT3G23940};
GN ORFNames=F14O13.13 {ECO:0000303|PubMed:10907853};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [4]
RP REVIEW, AND PATHWAY.
RX PubMed=12242394; DOI=10.2307/3870048;
RA Singh B.K., Shaner D.L.;
RT "Biosynthesis of branched chain amino acids: from test tube to field.";
RL Plant Cell 7:935-944(1995).
RN [5]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-35, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER CYS-34, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [6] {ECO:0007744|PDB:5YM0}
RP X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS).
RA Zang X., Huang W.X., Cheng R., Wu L., Zhou J.H.;
RT "The crystal structure of DHAD.";
RL Submitted (OCT-2017) to the PDB data bank.
RN [7] {ECO:0007744|PDB:5ZE4}
RP X-RAY CRYSTALLOGRAPHY (2.11 ANGSTROMS) OF 36-608, FUNCTION, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, AND COFACTOR.
RX PubMed=29995859; DOI=10.1038/s41586-018-0319-4;
RA Yan Y., Liu Q., Zang X., Yuan S., Bat-Erdene U., Nguyen C., Gan J.,
RA Zhou J., Jacobsen S.E., Tang Y.;
RT "Resistance-gene-directed discovery of a natural-product herbicide with a
RT new mode of action.";
RL Nature 559:415-418(2018).
CC -!- FUNCTION: Functions in the biosynthesis of branched-chain amino acids.
CC Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate
CC (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-
CC 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-
CC dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate),
CC the penultimate precursor to L-isoleucine and L-valine, respectively.
CC {ECO:0000269|PubMed:29995859}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate
CC + H2O; Xref=Rhea:RHEA:24809, ChEBI:CHEBI:11851, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:49072; EC=4.2.1.9;
CC Evidence={ECO:0000269|PubMed:29995859};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24810;
CC Evidence={ECO:0000305|PubMed:29995859};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-
CC oxopentanoate + H2O; Xref=Rhea:RHEA:27694, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:35146, ChEBI:CHEBI:49258; EC=4.2.1.9;
CC Evidence={ECO:0000250|UniProtKB:P05791};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27695;
CC Evidence={ECO:0000250|UniProtKB:P05791};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:29995859};
CC Note=Binds 1 [2Fe-2S] cluster per subunit.
CC {ECO:0000269|PubMed:29995859};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P9WKJ5};
CC -!- ACTIVITY REGULATION: Is highly competitively inhibited by the fungal
CC sesquiterpenoid aspterric acid, which is effective as a herbicide in
CC spray applications. {ECO:0000269|PubMed:29995859}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5.7 mM for (2R)-2,3-dihydroxy-3-methylbutanoate
CC {ECO:0000269|PubMed:29995859};
CC Note=kcat is 1.2 sec(-1) with (2R)-2,3-dihydroxy-3-methylbutanoate as
CC substrate. {ECO:0000269|PubMed:29995859};
CC -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; L-
CC isoleucine from 2-oxobutanoate: step 3/4.
CC {ECO:0000305|PubMed:12242394}.
CC -!- PATHWAY: Amino-acid biosynthesis; L-valine biosynthesis; L-valine from
CC pyruvate: step 3/4. {ECO:0000305|PubMed:12242394}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LIR4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LIR4-2; Sequence=VSP_056812;
CC -!- SIMILARITY: Belongs to the IlvD/Edd family. {ECO:0000305}.
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DR EMBL; AP001297; BAB03011.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76834.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76835.1; -; Genomic_DNA.
DR EMBL; AF446360; AAL48233.1; -; mRNA.
DR EMBL; BT000972; AAN41372.1; -; mRNA.
DR EMBL; AY039921; AAK64025.1; -; mRNA.
DR RefSeq; NP_001189959.1; NM_001203030.1. [Q9LIR4-2]
DR RefSeq; NP_189036.1; NM_113299.5. [Q9LIR4-1]
DR PDB; 5YM0; X-ray; 1.84 A; A=1-608.
DR PDB; 5ZE4; X-ray; 2.11 A; A=36-608.
DR PDBsum; 5YM0; -.
DR PDBsum; 5ZE4; -.
DR AlphaFoldDB; Q9LIR4; -.
DR SMR; Q9LIR4; -.
DR BioGRID; 7309; 22.
DR IntAct; Q9LIR4; 1.
DR STRING; 3702.AT3G23940.1; -.
DR iPTMnet; Q9LIR4; -.
DR MetOSite; Q9LIR4; -.
DR SwissPalm; Q9LIR4; -.
DR PaxDb; Q9LIR4; -.
DR PRIDE; Q9LIR4; -.
DR ProteomicsDB; 248587; -. [Q9LIR4-1]
DR EnsemblPlants; AT3G23940.1; AT3G23940.1; AT3G23940. [Q9LIR4-1]
DR EnsemblPlants; AT3G23940.2; AT3G23940.2; AT3G23940. [Q9LIR4-2]
DR GeneID; 821977; -.
DR Gramene; AT3G23940.1; AT3G23940.1; AT3G23940. [Q9LIR4-1]
DR Gramene; AT3G23940.2; AT3G23940.2; AT3G23940. [Q9LIR4-2]
DR KEGG; ath:AT3G23940; -.
DR Araport; AT3G23940; -.
DR TAIR; locus:2076116; AT3G23940.
DR eggNOG; KOG2448; Eukaryota.
DR HOGENOM; CLU_014271_4_2_1; -.
DR InParanoid; Q9LIR4; -.
DR OMA; TQGRNMA; -.
DR PhylomeDB; Q9LIR4; -.
DR BioCyc; ARA:AT3G23940-MON; -.
DR BRENDA; 4.2.1.9; 399.
DR UniPathway; UPA00047; UER00057.
DR UniPathway; UPA00049; UER00061.
DR PRO; PR:Q9LIR4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LIR4; baseline and differential.
DR Genevisible; Q9LIR4; 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:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005507; F:copper ion binding; HDA:TAIR.
DR GO; GO:0004160; F:dihydroxy-acid dehydratase activity; IBA:GO_Central.
DR GO; GO:0016836; F:hydro-lyase activity; TAS:TAIR.
DR GO; GO:0009082; P:branched-chain amino acid biosynthetic process; IMP:TAIR.
DR GO; GO:0009553; P:embryo sac development; IMP:TAIR.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0009555; P:pollen development; IMP:TAIR.
DR GO; GO:0009651; P:response to salt stress; IMP:TAIR.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR GO; GO:0009099; P:valine biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.50.30.80; -; 1.
DR HAMAP; MF_00012; IlvD; 1.
DR InterPro; IPR042096; Dihydro-acid_dehy_C.
DR InterPro; IPR004404; DihydroxyA_deHydtase.
DR InterPro; IPR000581; DiOHA_6PGluconate_deHydtase.
DR InterPro; IPR020558; DiOHA_6PGluconate_deHydtase_CS.
DR InterPro; IPR037237; IlvD/EDD_N.
DR Pfam; PF00920; ILVD_EDD; 1.
DR SUPFAM; SSF143975; SSF143975; 1.
DR TIGRFAMs; TIGR00110; ilvD; 1.
DR PROSITE; PS00886; ILVD_EDD_1; 1.
DR PROSITE; PS00887; ILVD_EDD_2; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Acetylation; Alternative splicing;
KW Amino-acid biosynthesis; Branched-chain amino acid biosynthesis;
KW Chloroplast; Iron; Iron-sulfur; Lyase; Magnesium; Metal-binding; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..34
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 35..608
FT /note="Dihydroxy-acid dehydratase, chloroplastic"
FT /id="PRO_0000430600"
FT ACT_SITE 523
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P9WKJ5"
FT BINDING 100
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:29995859,
FT ECO:0007744|PDB:5ZE4"
FT BINDING 132
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P9WKJ5"
FT BINDING 173
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:29995859,
FT ECO:0007744|PDB:5ZE4"
FT BINDING 174
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:29995859,
FT ECO:0007744|PDB:5ZE4"
FT BINDING 245
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:29995859,
FT ECO:0007744|PDB:5ZE4"
FT BINDING 497
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:29995859,
FT ECO:0007744|PDB:5ZE4"
FT MOD_RES 35
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 393..394
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:27862469"
FT /id="VSP_056812"
FT CONFLICT 259
FT /note="E -> G (in Ref. 3; AAK64025)"
FT /evidence="ECO:0000305"
FT TURN 55..57
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 58..61
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 67..75
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 87..92
FT /evidence="ECO:0007829|PDB:5YM0"
FT TURN 99..103
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 104..117
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 132..135
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 139..143
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 144..162
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 165..170
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 178..187
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 202..204
FT /evidence="ECO:0007829|PDB:5ZE4"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:5ZE4"
FT HELIX 211..222
FT /evidence="ECO:0007829|PDB:5ZE4"
FT HELIX 228..237
FT /evidence="ECO:0007829|PDB:5ZE4"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:5ZE4"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:5ZE4"
FT HELIX 250..260
FT /evidence="ECO:0007829|PDB:5YM0"
FT TURN 266..270
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 276..295
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 299..302
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 305..318
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 323..334
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 341..350
FT /evidence="ECO:0007829|PDB:5YM0"
FT TURN 358..360
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 361..363
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 365..370
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 373..383
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 396..398
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 399..403
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 414..416
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 423..426
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 428..431
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 433..436
FT /evidence="ECO:0007829|PDB:5ZE4"
FT STRAND 442..444
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 447..449
FT /evidence="ECO:0007829|PDB:5ZE4"
FT STRAND 451..462
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 463..472
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 474..477
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 481..484
FT /evidence="ECO:0007829|PDB:5YM0"
FT TURN 489..493
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 500..507
FT /evidence="ECO:0007829|PDB:5YM0"
FT TURN 511..513
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 515..522
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 530..532
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 538..540
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 543..546
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 552..556
FT /evidence="ECO:0007829|PDB:5YM0"
FT TURN 557..560
FT /evidence="ECO:0007829|PDB:5YM0"
FT STRAND 561..566
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 568..577
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 588..596
FT /evidence="ECO:0007829|PDB:5YM0"
FT HELIX 600..602
FT /evidence="ECO:0007829|PDB:5YM0"
SQ SEQUENCE 608 AA; 64914 MW; 017A5E0CD3CDFA69 CRC64;
MQATIFSPRA TLFPCKPLLP SHNVNSRRPS IISCSAQSVT ADPSPPITDT NKLNKYSSRI
TEPKSQGGSQ AILHGVGLSD DDLLKPQIGI SSVWYEGNTC NMHLLKLSEA VKEGVENAGM
VGFRFNTIGV SDAISMGTRG MCFSLQSRDL IADSIETVMS AQWYDGNISI PGCDKNMPGT
IMAMGRLNRP GIMVYGGTIK PGHFQDKTYD IVSAFQSYGE FVSGSISDEQ RKTVLHHSCP
GAGACGGMYT ANTMASAIEA MGMSLPYSSS IPAEDPLKLD ECRLAGKYLL ELLKMDLKPR
DIITPKSLRN AMVSVMALGG STNAVLHLIA IARSVGLELT LDDFQKVSDA VPFLADLKPS
GKYVMEDIHK IGGTPAVLRY LLELGLMDGD CMTVTGQTLA QNLENVPSLT EGQEIIRPLS
NPIKETGHIQ ILRGDLAPDG SVAKITGKEG LYFSGPALVF EGEESMLAAI SADPMSFKGT
VVVIRGEGPK GGPGMPEMLT PTSAIMGAGL GKECALLTDG RFSGGSHGFV VGHICPEAQE
GGPIGLIKNG DIITIDIGKK RIDTQVSPEE MNDRRKKWTA PAYKVNRGVL YKYIKNVQSA
SDGCVTDE
