IVD_RAT
ID IVD_RAT Reviewed; 424 AA.
AC P12007;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1990, sequence version 2.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=Isovaleryl-CoA dehydrogenase, mitochondrial;
DE Short=IVD;
DE EC=1.3.8.4 {ECO:0000269|PubMed:6401713};
DE AltName: Full=Butyryl-CoA dehydrogenase;
DE EC=1.3.8.1 {ECO:0000250|UniProtKB:P26440};
DE Flags: Precursor;
GN Name=Ivd;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND PROTEIN SEQUENCE OF 31-61; 66-76; 77-83;
RP 198-211; 212-230; 231-239 AND 261-272.
RX PubMed=2777793; DOI=10.1016/s0021-9258(18)71624-4;
RA Matsubara Y., Indo Y., Naito E., Ozasa H., Glassberg R., Vockley J.,
RA Ikeda Y., Kraus J., Tanaka K.;
RT "Molecular cloning and nucleotide sequence of cDNAs encoding the precursors
RT of rat long chain acyl-coenzyme A, short chain acyl-coenzyme A, and
RT isovaleryl-coenzyme A dehydrogenases. Sequence homology of four enzymes of
RT the acyl-CoA dehydrogenase family.";
RL J. Biol. Chem. 264:16321-16331(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Heart;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-48.
RX PubMed=3446585; DOI=10.1016/0888-7543(87)90053-x;
RA Kraus J.P., Matsubara Y., Barton D., Yang-Feng T.L., Glassberg R., Ito M.,
RA Ikeda Y., Mole J., Francke U., Tanaka K.;
RT "Isolation of cDNA clones coding for rat isovaleryl-CoA dehydrogenase and
RT assignment of the gene to human chromosome 15.";
RL Genomics 1:264-269(1987).
RN [4]
RP SUBCELLULAR LOCATION, COFACTOR, AND CATALYTIC ACTIVITY.
RX PubMed=6401713; DOI=10.1016/s0021-9258(18)33161-2;
RA Ikeda Y., Tanaka K.;
RT "Purification and characterization of isovaleryl coenzyme A dehydrogenase
RT from rat liver mitochondria.";
RL J. Biol. Chem. 258:1077-1085(1983).
RN [5]
RP PROTEIN SEQUENCE OF 119-140; 273-285 AND 400-411, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RC STRAIN=Sprague-Dawley; TISSUE=Hippocampus, and Spinal cord;
RA Lubec G., Afjehi-Sadat L., Chen W.-Q.;
RL Submitted (APR-2007) to UniProtKB.
CC -!- FUNCTION: Catalyzes the conversion of isovaleryl-CoA/3-methylbutanoyl-
CC CoA to 3-methylbut-2-enoyl-CoA as an intermediate step in the leucine
CC (Leu) catabolic pathway. To a lesser extent, is also able to catalyze
CC the oxidation of other saturated short-chain acyl-CoA thioesters as
CC pentanoyl-CoA, hexenoyl-CoA and butenoyl-CoA.
CC {ECO:0000250|UniProtKB:P26440}.
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:6401713};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + oxidized [electron-transfer flavoprotein] + pentanoyl-
CC CoA = (2E)-pentenoyl-CoA + reduced [electron-transfer flavoprotein];
CC Xref=Rhea:RHEA:43456, Rhea:RHEA-COMP:10685, Rhea:RHEA-COMP:10686,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57389, ChEBI:CHEBI:57692,
CC ChEBI:CHEBI:58307, ChEBI:CHEBI:86160;
CC Evidence={ECO:0000250|UniProtKB:P26440};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + hexanoyl-CoA + oxidized [electron-transfer
CC flavoprotein] = (2E)-hexenoyl-CoA + reduced [electron-transfer
CC flavoprotein]; Xref=Rhea:RHEA:43464, Rhea:RHEA-COMP:10685, Rhea:RHEA-
CC COMP:10686, ChEBI:CHEBI:15378, ChEBI:CHEBI:57692, ChEBI:CHEBI:58307,
CC ChEBI:CHEBI:62077, ChEBI:CHEBI:62620;
CC Evidence={ECO:0000250|UniProtKB:P26440};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=butanoyl-CoA + H(+) + oxidized [electron-transfer
CC flavoprotein] = (2E)-butenoyl-CoA + reduced [electron-transfer
CC flavoprotein]; Xref=Rhea:RHEA:24004, Rhea:RHEA-COMP:10685, Rhea:RHEA-
CC COMP:10686, ChEBI:CHEBI:15378, ChEBI:CHEBI:57332, ChEBI:CHEBI:57371,
CC ChEBI:CHEBI:57692, ChEBI:CHEBI:58307; EC=1.3.8.1;
CC Evidence={ECO:0000250|UniProtKB:P26440};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:6401713};
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:0000250|UniProtKB:P26440}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC {ECO:0000269|PubMed:6401713}.
CC -!- SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; J05031; AAA41454.1; -; mRNA.
DR EMBL; BC088401; AAH88401.1; -; mRNA.
DR EMBL; M19867; AAA41459.1; -; mRNA.
DR PIR; C34252; C34252.
DR RefSeq; NP_036724.1; NM_012592.2.
DR AlphaFoldDB; P12007; -.
DR SMR; P12007; -.
DR BioGRID; 246669; 2.
DR IntAct; P12007; 2.
DR STRING; 10116.ENSRNOP00000013829; -.
DR iPTMnet; P12007; -.
DR PhosphoSitePlus; P12007; -.
DR jPOST; P12007; -.
DR PaxDb; P12007; -.
DR PRIDE; P12007; -.
DR Ensembl; ENSRNOT00000013829; ENSRNOP00000013829; ENSRNOG00000009421.
DR GeneID; 24513; -.
DR KEGG; rno:24513; -.
DR UCSC; RGD:2936; rat.
DR CTD; 3712; -.
DR RGD; 2936; Ivd.
DR eggNOG; KOG0141; Eukaryota.
DR GeneTree; ENSGT00940000158100; -.
DR HOGENOM; CLU_018204_0_1_1; -.
DR InParanoid; P12007; -.
DR OMA; CFITNSG; -.
DR OrthoDB; 589058at2759; -.
DR PhylomeDB; P12007; -.
DR TreeFam; TF105050; -.
DR BRENDA; 1.3.8.4; 5301.
DR Reactome; R-RNO-70895; Branched-chain amino acid catabolism.
DR SABIO-RK; P12007; -.
DR UniPathway; UPA00363; UER00860.
DR PRO; PR:P12007; -.
DR Proteomes; UP000002494; Chromosome 3.
DR Bgee; ENSRNOG00000009421; Expressed in heart and 20 other tissues.
DR Genevisible; P12007; RN.
DR GO; GO:0005759; C:mitochondrial matrix; IDA:BHF-UCL.
DR GO; GO:0031966; C:mitochondrial membrane; IDA:BHF-UCL.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0003995; F:acyl-CoA dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0004085; F:butyryl-CoA dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0042802; F:identical protein binding; IPI:RGD.
DR GO; GO:0008470; F:isovaleryl-CoA dehydrogenase activity; IDA:BHF-UCL.
DR GO; GO:0009083; P:branched-chain amino acid catabolic process; ISO:RGD.
DR GO; GO:0033539; P:fatty acid beta-oxidation using acyl-CoA dehydrogenase; ISO:RGD.
DR GO; GO:0006552; P:leucine catabolic process; IDA:BHF-UCL.
DR GO; GO:0006551; P:leucine metabolic process; TAS:RGD.
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 Acetylation; Direct protein sequencing; FAD; Flavoprotein; Mitochondrion;
KW Oxidoreductase; Reference proteome; Transit peptide.
FT TRANSIT 1..30
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:2777793"
FT CHAIN 31..424
FT /note="Isovaleryl-CoA dehydrogenase, mitochondrial"
FT /id="PRO_0000000534"
FT ACT_SITE 284
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 163..172
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 172
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 196..198
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 220..221
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 275
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 282..285
FT /ligand="substrate"
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 321
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 378..382
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 405..406
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT BINDING 407..409
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT MOD_RES 56
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 56
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 65
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 65
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 76
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P26440"
FT MOD_RES 76
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 239
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 260
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 260
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
FT MOD_RES 316
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9JHI5"
SQ SEQUENCE 424 AA; 46435 MW; D09FFD0A88EA5791 CRC64;
MATAVRLLGR RVSSWRLRPL PSPLAVPQRA HSMLPVDDDI NGLNEEQKQL RHTISKFVQE
NLAPKAQEID QSNDFKNLRE FWKQLGSLGV LGITAPVQYG GSGLGYLEHV LVMEEISRAS
AAVGLSYGAH SNLCINQIVR NGNEAQKEKY LPKLISGEFI GALAMSEPNA GSDVVSMRLK
AEKKGDHYVL NGNKFWITNG PDADVLVVYA KTDLTAVPAS RGITAFIVEK DMPGFSTSKK
LDKLGMRGSN TCELVFEDCK VPAANILSQE SKGVYVLMSG LDLERLVLAG GPLGIMQAVL
DHTIPYLHVR EAFGQKIGQF QLMQGKMADM YTRLMACRQY VYNVARACDE GHITAKDCAG
VILYTAECAT QVALDGIQCL GGNGYINDFP MGRFLRDAKL YEIGGGTSEV RRLVIGRAFN
ADFR
