DLDH2_ARATH
ID DLDH2_ARATH Reviewed; 507 AA.
AC Q9M5K2; Q8LBH6; Q9ZRQ0;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=Dihydrolipoyl dehydrogenase 2, mitochondrial;
DE Short=AtmLPD2;
DE Short=mtLPD2;
DE EC=1.8.1.4 {ECO:0000269|PubMed:11598235};
DE AltName: Full=Dihydrolipoamide dehydrogenase 2;
DE AltName: Full=Glycine cleavage system L protein 2;
DE AltName: Full=Pyruvate dehydrogenase complex E3 subunit 2;
DE Short=E3-2;
DE Short=PDC-E3 2;
DE Flags: Precursor;
GN Name=LPD2; OrderedLocusNames=At3g17240; ORFNames=MGD8.7;
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 [MRNA] (ISOFORM 1), FUNCTION, CATALYTIC ACTIVITY,
RP TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=11598235; DOI=10.1104/pp.010321;
RA Lutziger I., Oliver D.J.;
RT "Characterization of two cDNAs encoding mitochondrial lipoamide
RT dehydrogenase from Arabidopsis.";
RL Plant Physiol. 127:615-623(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
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] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 36-507 (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Machuy N., Klein M., Mueller-Roeber B.;
RT "Cloning and characterization of 2-oxoglutarate dehydrogenase from
RT Arabidopsis thaliana.";
RL Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP REVIEW.
RX PubMed=11286922; DOI=10.1016/s1360-1385(01)01892-1;
RA Douce R., Bourguignon J., Neuburger M., Rebeille F.;
RT "The glycine decarboxylase system: a fascinating complex.";
RL Trends Plant Sci. 6:167-176(2001).
RN [8]
RP REVIEW, AND NOMENCLATURE.
RX PubMed=12730263; DOI=10.1093/jxb/erg171;
RA Bauwe H., Kolukisaoglu U.;
RT "Genetic manipulation of glycine decarboxylation.";
RL J. Exp. Bot. 54:1523-1535(2003).
RN [9]
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 [10]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
RX PubMed=14764908; DOI=10.1104/pp.103.035675;
RA Taylor N.L., Heazlewood J.L., Day D.A., Millar A.H.;
RT "Lipoic acid-dependent oxidative catabolism of alpha-keto acids in
RT mitochondria provides evidence for branched-chain amino acid catabolism in
RT Arabidopsis.";
RL Plant Physiol. 134:838-848(2004).
RN [11]
RP INDUCTION BY CADMIUM.
RC STRAIN=cv. Columbia;
RX PubMed=16502469; DOI=10.1002/pmic.200500543;
RA Sarry J.-E., Kuhn L., Ducruix C., Lafaye A., Junot C., Hugouvieux V.,
RA Jourdain A., Bastien O., Fievet J.B., Vailhen D., Amekraz B., Moulin C.,
RA Ezan E., Garin J., Bourguignon J.;
RT "The early responses of Arabidopsis thaliana cells to cadmium exposure
RT explored by protein and metabolite profiling analyses.";
RL Proteomics 6:2180-2198(2006).
RN [12]
RP S-NITROSYLATION.
RX PubMed=20089767; DOI=10.1104/pp.109.152579;
RA Palmieri M.C., Lindermayr C., Bauwe H., Steinhauser C., Durner J.;
RT "Regulation of plant glycine decarboxylase by s-nitrosylation and
RT glutathionylation.";
RL Plant Physiol. 152:1514-1528(2010).
RN [13]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP PHE-36.
RX PubMed=25732537; DOI=10.1093/jxb/erv064;
RA Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT "Identification of cleavage sites and substrate proteins for two
RT mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL J. Exp. Bot. 66:2691-2708(2015).
CC -!- FUNCTION: Lipoamide dehydrogenase is a component of the glycine
CC decarboxylase (GDC) or glycine cleavage system as well as of the alpha-
CC ketoacid dehydrogenase complexes. LPD1 is probably the protein most
CC often associated with the glycine decarboxylase complex while LPD2 is
CC probably incorporated into alpha-ketoacid dehydrogenase complexes.
CC {ECO:0000269|PubMed:11598235, ECO:0000269|PubMed:14764908}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NAD(+) = (R)-N(6)-
CC lipoyl-L-lysyl-[protein] + H(+) + NADH; Xref=Rhea:RHEA:15045,
CC Rhea:RHEA-COMP:10474, Rhea:RHEA-COMP:10475, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:83099,
CC ChEBI:CHEBI:83100; EC=1.8.1.4;
CC Evidence={ECO:0000269|PubMed:11598235};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
CC Note=Binds 1 FAD per subunit. {ECO:0000250};
CC -!- SUBUNIT: Homodimer (By similarity). Part of both the glycine cleavage
CC system composed of four proteins: P, T, L and H and of the pyruvate
CC dehydrogenase complex containing multiple copies of three enzymatic
CC components: pyruvate dehydrogenase (E1), dihydrolipoamide
CC acetyltransferase (E2) and lipoamide dehydrogenase (E3). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC {ECO:0000269|PubMed:14671022, ECO:0000269|PubMed:14764908,
CC ECO:0000305|PubMed:25732537}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9M5K2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9M5K2-2; Sequence=VSP_021588, VSP_021589;
CC -!- TISSUE SPECIFICITY: Preferentially expressed in roots, flowers and
CC siliques and at a lower level in stems and leaves.
CC {ECO:0000269|PubMed:11598235}.
CC -!- INDUCTION: Induced by cadmium. {ECO:0000269|PubMed:16502469}.
CC -!- PTM: S-nytrosylated at unknown positions.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype, probably due to redundancy
CC with LPD1. {ECO:0000269|PubMed:11598235}.
CC -!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to an intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
CC oxidoreductase family. {ECO:0000305}.
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DR EMBL; AF228640; AAF34796.1; -; mRNA.
DR EMBL; AB022216; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002686; AEE75925.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75926.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75927.1; -; Genomic_DNA.
DR EMBL; BT024578; ABD38917.1; -; mRNA.
DR EMBL; AY087203; AAM64759.1; -; mRNA.
DR EMBL; AJ223804; CAA11554.1; -; mRNA.
DR RefSeq; NP_566570.3; NM_112601.3. [Q9M5K2-1]
DR RefSeq; NP_566571.1; NM_112602.2. [Q9M5K2-2]
DR RefSeq; NP_851005.1; NM_180674.4. [Q9M5K2-1]
DR AlphaFoldDB; Q9M5K2; -.
DR SMR; Q9M5K2; -.
DR BioGRID; 6317; 8.
DR IntAct; Q9M5K2; 1.
DR STRING; 3702.AT3G17240.1; -.
DR iPTMnet; Q9M5K2; -.
DR MetOSite; Q9M5K2; -.
DR PaxDb; Q9M5K2; -.
DR PRIDE; Q9M5K2; -.
DR ProteomicsDB; 222210; -. [Q9M5K2-1]
DR EnsemblPlants; AT3G17240.1; AT3G17240.1; AT3G17240. [Q9M5K2-1]
DR EnsemblPlants; AT3G17240.2; AT3G17240.2; AT3G17240. [Q9M5K2-2]
DR EnsemblPlants; AT3G17240.3; AT3G17240.3; AT3G17240. [Q9M5K2-1]
DR GeneID; 820984; -.
DR Gramene; AT3G17240.1; AT3G17240.1; AT3G17240. [Q9M5K2-1]
DR Gramene; AT3G17240.2; AT3G17240.2; AT3G17240. [Q9M5K2-2]
DR Gramene; AT3G17240.3; AT3G17240.3; AT3G17240. [Q9M5K2-1]
DR KEGG; ath:AT3G17240; -.
DR Araport; AT3G17240; -.
DR TAIR; locus:2089030; AT3G17240.
DR eggNOG; KOG1335; Eukaryota.
DR HOGENOM; CLU_016755_0_1_1; -.
DR InParanoid; Q9M5K2; -.
DR OMA; QAMPFVI; -.
DR OrthoDB; 581771at2759; -.
DR PhylomeDB; Q9M5K2; -.
DR BRENDA; 1.8.1.4; 399.
DR PRO; PR:Q9M5K2; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M5K2; baseline and differential.
DR Genevisible; Q9M5K2; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
DR GO; GO:0005747; C:mitochondrial respiratory chain complex I; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0045252; C:oxoglutarate dehydrogenase complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; HDA:TAIR.
DR GO; GO:0050897; F:cobalt ion binding; HDA:TAIR.
DR GO; GO:0005507; F:copper ion binding; HDA:TAIR.
DR GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IMP:TAIR.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; HDA:TAIR.
DR GO; GO:0045454; P:cell redox homeostasis; IEA:InterPro.
DR Gene3D; 3.30.390.30; -; 1.
DR Gene3D; 3.50.50.60; -; 2.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR023753; FAD/NAD-binding_dom.
DR InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer_sf.
DR InterPro; IPR006258; Lipoamide_DH.
DR InterPro; IPR001100; Pyr_nuc-diS_OxRdtase.
DR InterPro; IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
DR InterPro; IPR012999; Pyr_OxRdtase_I_AS.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR Pfam; PF02852; Pyr_redox_dim; 1.
DR PIRSF; PIRSF000350; Mercury_reductase_MerA; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR SUPFAM; SSF55424; SSF55424; 1.
DR TIGRFAMs; TIGR01350; lipoamide_DH; 1.
DR PROSITE; PS00076; PYRIDINE_REDOX_1; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Disulfide bond; FAD; Flavoprotein; Mitochondrion;
KW NAD; Oxidoreductase; Redox-active center; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..36
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537"
FT CHAIN 37..507
FT /note="Dihydrolipoyl dehydrogenase 2, mitochondrial"
FT /id="PRO_0000260230"
FT ACT_SITE 486
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 73..82
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 91
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 155
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 184..186
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 221..228
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 244
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 278
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 313
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 354
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 360..363
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT DISULFID 82..87
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT VAR_SEQ 92..127
FT /note="ALLHSSHMYHEAKHVFANHGVKVSSVEVDLPAMLAQ -> VILETPFPITLI
FT RRKFSPIFIRLLWNLLVDHHLDSI (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4, ECO:0000303|Ref.5"
FT /id="VSP_021588"
FT VAR_SEQ 128..507
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4, ECO:0000303|Ref.5"
FT /id="VSP_021589"
SQ SEQUENCE 507 AA; 53986 MW; C5CA38074A8103D7 CRC64;
MAMASLARRK AYFLTRNISN SPTDAFRFSF SLTRGFASSG SDDNDVVIIG GGPGGYVAAI
KAAQLGLKTT CIEKRGALGG TCLNVGCIPS KALLHSSHMY HEAKHVFANH GVKVSSVEVD
LPAMLAQKDT AVKNLTRGVE GLFKKNKVNY VKGYGKFLSP SEVSVDTIDG ENVVVKGKHI
IVATGSDVKS LPGITIDEKK IVSSTGALSL TEIPKKLIVI GAGYIGLEMG SVWGRLGSEV
TVVEFAADIV PAMDGEIRKQ FQRSLEKQKM KFMLKTKVVG VDSSGDGVKL IVEPAEGGEQ
TTLEADVVLV SAGRTPFTSG LDLEKIGVET DKGGRILVNE RFSTNVSGVY AIGDVIPGPM
LAHKAEEDGV ACVEFIAGKH GHVDYDKVPG VVYTYPEVAS VGKTEEQLKK EGVSYNVGKF
PFMANSRAKA IDTAEGMVKI LADKETDKIL GVHIMSPNAG ELIHEAVLAI NYDASSEDIA
RVCHAHPTMS EAIKEAAMAT YDKPIHM
