IVD_SOLTU
ID IVD_SOLTU Reviewed; 412 AA.
AC Q9FS87; M1AEC9;
DT 25-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 24-JUL-2013, sequence version 2.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Isovaleryl-CoA dehydrogenase, mitochondrial;
DE Short=IVD;
DE EC=1.3.8.4;
DE AltName: Full=Isovaleryl-CoA dehydrogenase 2;
DE Short=St-IVD2;
DE Flags: Precursor;
GN Name=IVD; Synonyms=IVD2; ORFNames=PGSC0003DMG400008113;
OS Solanum tuberosum (Potato).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum.
OX NCBI_TaxID=4113;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. DM1-3 516 R44;
RX PubMed=21743474; DOI=10.1038/nature10158;
RG The Potato Genome Sequencing Consortium;
RT "Genome sequence and analysis of the tuber crop potato.";
RL Nature 475:189-195(2011).
RN [2] {ECO:0000305}
RP NUCLEOTIDE SEQUENCE [MRNA] OF 12-412, PROTEIN SEQUENCE OF 29-55, FUNCTION,
RP CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBCELLULAR LOCATION, AND TISSUE
RP SPECIFICITY.
RC STRAIN=cv. Bintje; TISSUE=Tuber;
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 FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=15574432; DOI=10.1074/jbc.m412640200;
RA Goetzman E.S., Mohsen A.W., Prasad K., Vockley J.;
RT "Convergent evolution of a 2-methylbutyryl-CoA dehydrogenase from
RT isovaleryl-CoA dehydrogenase in Solanum tuberosum.";
RL J. Biol. Chem. 280:4873-4879(2005).
CC -!- FUNCTION: Involved in the catabolism of amino acids. Uses isovaleryl-
CC CoA as substrate. Minor activity detected with 2-methylpalmitoyl-CoA or
CC 2-methylbutanoyl-CoA, but no activity with short- and medium-straight
CC chain acyl-CoA esters or with 2-methylhexanoyl-CoA.
CC {ECO:0000269|PubMed:11231285, ECO:0000269|PubMed:15574432}.
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, ECO:0000269|PubMed:15574432};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000250|UniProtKB:P26440};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.3 uM for Isovaleryl-CoA {ECO:0000269|PubMed:15574432};
CC Note=kcat is 0.98 sec(-1) per tetramer for Isovaleryl-CoA.;
CC -!- PATHWAY: Amino-acid degradation; L-leucine degradation; (S)-3-hydroxy-
CC 3-methylglutaryl-CoA from 3-isovaleryl-CoA: step 1/3.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:15574432}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:11231285}.
CC -!- TISSUE SPECIFICITY: Expressed in flowers and tubers.
CC {ECO:0000269|PubMed:11231285}.
CC -!- MISCELLANEOUS: Was previously thought to be duplicated, but
CC PubMed:15574432 showed that the protein encoded by the second gene
CC (2MBCD) is a 2-methylbutanoyl-CoA dehydrogenase.
CC {ECO:0000305|PubMed:11231285}.
CC -!- SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; AJ278988; CAC08234.1; -; mRNA.
DR RefSeq; XP_006340144.1; XM_006340082.2.
DR AlphaFoldDB; Q9FS87; -.
DR SMR; Q9FS87; -.
DR IntAct; Q9FS87; 1.
DR STRING; 4113.PGSC0003DMT400020955; -.
DR EnsemblPlants; PGSC0003DMT400020955; PGSC0003DMT400020955; PGSC0003DMG400008113.
DR GeneID; 102601763; -.
DR Gramene; PGSC0003DMT400020955; PGSC0003DMT400020955; PGSC0003DMG400008113.
DR KEGG; sot:102601763; -.
DR eggNOG; KOG0141; Eukaryota.
DR HOGENOM; CLU_018204_0_1_1; -.
DR InParanoid; Q9FS87; -.
DR OMA; CFITNSG; -.
DR OrthoDB; 589058at2759; -.
DR BRENDA; 1.3.8.4; 5757.
DR SABIO-RK; Q9FS87; -.
DR UniPathway; UPA00363; UER00860.
DR Proteomes; UP000011115; Unassembled WGS sequence.
DR ExpressionAtlas; Q9FS87; baseline.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0003995; F:acyl-CoA dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0008470; F:isovaleryl-CoA dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:1902198; P:3-methylbut-2-enoyl-CoA(4-) metabolic process; IDA:UniProtKB.
DR GO; GO:1902196; P:isovaleryl-CoA(4-) catabolic process; IDA:UniProtKB.
DR GO; GO:0006552; P:leucine catabolic process; IBA:GO_Central.
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 Direct protein sequencing; FAD; Flavoprotein; Mitochondrion;
KW Oxidoreductase; Reference proteome; Transit peptide.
FT TRANSIT 1..25
FT /note="Mitochondrion"
FT /evidence="ECO:0000305"
FT CHAIN 26..412
FT /note="Isovaleryl-CoA dehydrogenase, mitochondrial"
FT /id="PRO_0000000537"
FT ACT_SITE 273
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 154..163
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 163
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 187..189
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 209..210
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 264
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 271..274
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 299
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 310
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 367..371
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 394..395
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 396..398
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT CONFLICT 78
FT /note="N -> D (in Ref. 2; CAC08234)"
FT /evidence="ECO:0000305"
FT CONFLICT 160
FT /note="N -> D (in Ref. 2; CAC08234)"
FT /evidence="ECO:0000305"
FT CONFLICT 208
FT /note="G -> S (in Ref. 2; CAC08234)"
FT /evidence="ECO:0000305"
FT CONFLICT 261
FT /note="R -> K (in Ref. 2; CAC08234)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 412 AA; 45264 MW; 34903F0ED45DE3EA CRC64;
MHKLFVARSV KSALFRIKNH QKPQFAAFST SLLFDDTQKQ FKESVAQFAQ ENIAPHAEKI
DRTNYFPQDV NLWKLMGNFN LLGITVPEEY GGLGLGYLYH CIAMEEISRA SGSVGLSYGA
HTNLCINQLV RNGTHEQKQK YLPKLISGEH VGALAMSEPN AGSDVVSMKC KADRVEGGYV
LNGNKMWCTN GPTAQTLVVY AKTDVTAGSK GITAFIIEKG MTGFSTAQKL DKLGMRGSDT
CELVFENCFV PEENVLGQVG RGVYVLMSGL DLERLVLASG PVGIMQACLD VVLPYVKQRE
QFGRPIGEFQ FVQGKVADMY TSMQSSRSYL YSVARECDSG TINTKDCAGV ILSAAERATQ
VALQAIQCLG GNGYVNEYPT GRFLRDAKLY EIGAGTSEIR RMIIGRELFK EQ
