IVD_ARATH
ID IVD_ARATH Reviewed; 409 AA.
AC Q9SWG0; Q8W4G7; Q9XFT2;
DT 15-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=Isovaleryl-CoA dehydrogenase, mitochondrial;
DE Short=IVD;
DE EC=1.3.8.4;
DE Flags: Precursor;
GN Name=IVD; OrderedLocusNames=At3g45300; ORFNames=F18N11.6;
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 {ECO:0000312|EMBL:AAD45605.1};
RN [1] {ECO:0000305}
RP NUCLEOTIDE SEQUENCE [MRNA], AND SUBCELLULAR LOCATION.
RX PubMed=10380813; DOI=10.1023/a:1006129220778;
RA Daeschner K., Thalheim C., Guha C., Brennicke A., Binder S.;
RT "In plants a putative isovaleryl-CoA-dehydrogenase is located in
RT mitochondria.";
RL Plant Mol. Biol. 39:1275-1282(1999).
RN [2] {ECO:0000305}
RP NUCLEOTIDE SEQUENCE [MRNA], SUBUNIT, CATALYTIC ACTIVITY, AND TISSUE
RP SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=11231285; DOI=10.1046/j.1432-1327.2001.01999.x;
RA Faivre-Nitschke S.E., Couee I., Vermel M., Grienenberger J.-M.,
RA Gualberto J.M.;
RT "Purification, characterization and cloning of isovaleryl-CoA dehydrogenase
RT from higher plant mitochondria.";
RL Eur. J. Biochem. 268:1332-1339(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [4] {ECO:0000312|EMBL:CAB72479.1}
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 [5]
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 [6] {ECO:0000312|EMBL:CAB72479.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=20501910; DOI=10.1105/tpc.110.075630;
RA Araujo W.L., Ishizaki K., Nunes-Nesi A., Larson T.R., Tohge T.,
RA Krahnert I., Witt S., Obata T., Schauer N., Graham I.A., Leaver C.J.,
RA Fernie A.R.;
RT "Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases
RT as alternative electron donors linking lysine catabolism to the electron
RT transport chain of Arabidopsis mitochondria.";
RL Plant Cell 22:1549-1563(2010).
CC -!- FUNCTION: Involved in degradation of the branched-chain amino acids,
CC phytol and lysine for the supply of carbon and electrons to the
CC ETF/ETFQO complex during dark-induced sugar starvation.
CC {ECO:0000269|PubMed:20501910}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-methylbutanoyl-CoA + H(+) + oxidized [electron-transfer
CC flavoprotein] = 3-methyl-(2E)-butenoyl-CoA + reduced [electron-
CC transfer flavoprotein]; Xref=Rhea:RHEA:12276, Rhea:RHEA-COMP:10685,
CC Rhea:RHEA-COMP:10686, ChEBI:CHEBI:15378, ChEBI:CHEBI:57344,
CC ChEBI:CHEBI:57345, ChEBI:CHEBI:57692, ChEBI:CHEBI:58307; EC=1.3.8.4;
CC Evidence={ECO:0000269|PubMed:11231285};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000250|UniProtKB:P26440};
CC -!- PATHWAY: Amino-acid degradation; L-leucine degradation; (S)-3-hydroxy-
CC 3-methylglutaryl-CoA from 3-isovaleryl-CoA: step 1/3.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11231285}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:10380813,
CC ECO:0000269|PubMed:14671022}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, stems and flowers. Not
CC detected in roots. {ECO:0000269|PubMed:11231285}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:20501910}.
CC -!- SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; Y12695; CAA73227.1; -; mRNA.
DR EMBL; AF160729; AAD45605.1; -; mRNA.
DR EMBL; AL132953; CAB72479.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78020.1; -; Genomic_DNA.
DR EMBL; AY062567; AAL32645.1; -; mRNA.
DR EMBL; AY128799; AAM91199.1; -; mRNA.
DR EMBL; AY087286; AAM64839.1; -; mRNA.
DR PIR; T47470; T47470.
DR RefSeq; NP_190116.1; NM_114399.5.
DR AlphaFoldDB; Q9SWG0; -.
DR SMR; Q9SWG0; -.
DR BioGRID; 8988; 3.
DR STRING; 3702.AT3G45300.1; -.
DR PaxDb; Q9SWG0; -.
DR PRIDE; Q9SWG0; -.
DR ProteomicsDB; 232283; -.
DR EnsemblPlants; AT3G45300.1; AT3G45300.1; AT3G45300.
DR GeneID; 823668; -.
DR Gramene; AT3G45300.1; AT3G45300.1; AT3G45300.
DR KEGG; ath:AT3G45300; -.
DR Araport; AT3G45300; -.
DR TAIR; locus:2078302; AT3G45300.
DR eggNOG; KOG0141; Eukaryota.
DR HOGENOM; CLU_018204_0_1_1; -.
DR InParanoid; Q9SWG0; -.
DR OMA; CFITNSG; -.
DR OrthoDB; 589058at2759; -.
DR PhylomeDB; Q9SWG0; -.
DR BioCyc; ARA:AT3G45300-MON; -.
DR BRENDA; 1.3.8.4; 399.
DR UniPathway; UPA00363; UER00860.
DR PRO; PR:Q9SWG0; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SWG0; baseline and differential.
DR Genevisible; Q9SWG0; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005759; C:mitochondrial matrix; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0003995; F:acyl-CoA dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; HDA:TAIR.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0008470; F:isovaleryl-CoA dehydrogenase activity; IDA:TAIR.
DR GO; GO:0010230; P:alternative respiration; IMP:TAIR.
DR GO; GO:0009083; P:branched-chain amino acid catabolic process; IMP:TAIR.
DR GO; GO:0006552; P:leucine catabolic process; IDA:TAIR.
DR CDD; cd01156; IVD; 1.
DR Gene3D; 1.10.540.10; -; 1.
DR Gene3D; 2.40.110.10; -; 1.
DR InterPro; IPR006089; Acyl-CoA_DH_CS.
DR InterPro; IPR006091; Acyl-CoA_Oxase/DH_mid-dom.
DR InterPro; IPR046373; Acyl-CoA_Oxase/DH_mid-dom_sf.
DR InterPro; IPR036250; AcylCo_DH-like_C.
DR InterPro; IPR009075; AcylCo_DH/oxidase_C.
DR InterPro; IPR013786; AcylCoA_DH/ox_N.
DR InterPro; IPR037069; AcylCoA_DH/ox_N_sf.
DR InterPro; IPR009100; AcylCoA_DH/oxidase_NM_dom.
DR InterPro; IPR034183; IVD.
DR Pfam; PF00441; Acyl-CoA_dh_1; 1.
DR Pfam; PF02770; Acyl-CoA_dh_M; 1.
DR Pfam; PF02771; Acyl-CoA_dh_N; 1.
DR SUPFAM; SSF47203; SSF47203; 1.
DR SUPFAM; SSF56645; SSF56645; 1.
DR PROSITE; PS00072; ACYL_COA_DH_1; 1.
DR PROSITE; PS00073; ACYL_COA_DH_2; 1.
PE 1: Evidence at protein level;
KW FAD; Flavoprotein; Mitochondrion; Oxidoreductase; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..22
FT /note="Mitochondrion"
FT /evidence="ECO:0000305"
FT CHAIN 23..409
FT /note="Isovaleryl-CoA dehydrogenase, mitochondrial"
FT /id="PRO_0000000535"
FT ACT_SITE 270
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 151..160
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 160
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 184..186
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 206..207
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 261
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 268..271
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 296
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 307
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 364..368
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 391..392
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 393..395
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT CONFLICT 49
FT /note="N -> I (in Ref. 2; AAD45605 and 6; AAM64839)"
FT /evidence="ECO:0000305"
FT CONFLICT 282
FT /note="M -> V (in Ref. 5; AAL32645/AAM91199)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 409 AA; 44773 MW; 6D3D86C8F632067C CRC64;
MQRFFSARSI LGYAVKTRRR SFSSRSSSLL FDDTQLQFKE SVSKFAQDNI APHAERIDKT
NSFPKDVNLW KLMGEFNLHG ITAPEEYGGL GLGYLYHCIA MEEISRASGS VALSYGAHSN
LCINQLVRNG TAAQKEKYLP KLISGEHVGA LAMSEPNAGS DVVGMKCKAE KVDGGYILNG
NKMWCTNGPS AETLVVYAKT DTKAGSKGIT AFIIEKGMTG FSTAQKLDKL GMRGSDTCEL
VFENCFVPEE NILDKEGKGV YVLMSGLDLE RLVLAAGPLG IMQACLDNVL PYIRQREQFG
RPVGEFQFIQ GKVADMYTAL QSSRSYVYSV ARDCDNGKVD PKDCAGTILC AAERATQVAL
QAIQCLGGNG YINEYATGRL LRDAKLYEIG AGTSEIRRIV IGRELFKEE
