PLPD1_ARATH
ID PLPD1_ARATH Reviewed; 623 AA.
AC A8MS68; B9DG34; Q9M5K5;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 1.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Dihydrolipoyl dehydrogenase 1, chloroplastic;
DE Short=ptLPD1;
DE EC=1.8.1.4;
DE AltName: Full=Dihydrolipoamide dehydrogenase 1;
DE AltName: Full=Protein LIPOAMIDE DEHYDROGENASE 1;
DE AltName: Full=Pyruvate dehydrogenase complex E3 subunit 1;
DE Short=E3-1;
DE Short=PDC-E3 1;
DE Flags: Precursor;
GN Name=LPD1; OrderedLocusNames=At3g16950; ORFNames=K14A17.6;
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;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, SUBCELLULAR LOCATION, AND
RP TISSUE SPECIFICITY.
RX PubMed=11056213; DOI=10.1016/s0014-5793(00)02116-5;
RA Lutziger I., Oliver D.J.;
RT "Molecular evidence of a unique lipoamide dehydrogenase in plastids:
RT analysis of plastidic lipoamide dehydrogenase from Arabidopsis thaliana.";
RL FEBS Lett. 484:12-16(2000).
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;
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP DISRUPTION PHENOTYPE.
RX PubMed=20488895; DOI=10.1104/pp.110.153452;
RA Chen W., Chi Y., Taylor N.L., Lambers H., Finnegan P.M.;
RT "Disruption of ptLPD1 or ptLPD2, genes that encode isoforms of the
RT plastidial lipoamide dehydrogenase, confers arsenate hypersensitivity in
RT Arabidopsis.";
RL Plant Physiol. 153:1385-1397(2010).
CC -!- FUNCTION: Lipoamide dehydrogenase is a component of the plastidial
CC pyruvate dehydrogenase complex (PDC). {ECO:0000269|PubMed:11056213}.
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 -!- 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 the plastidial pyruvate
CC dehydrogenase complex (PDC) containing multiple copies of three
CC enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide
CC acetyltransferase (E2) and lipoamide dehydrogenase (E3). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:11056213}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=A8MS68-1; Sequence=Displayed;
CC Name=2;
CC IsoId=A8MS68-2; Sequence=VSP_047927, VSP_047928;
CC -!- TISSUE SPECIFICITY: Expressed mainly in flower buds and immature
CC siliques, and to a lesser extent in flowers.
CC {ECO:0000269|PubMed:11056213}.
CC -!- DISRUPTION PHENOTYPE: Arsenate hypersensitivity.
CC {ECO:0000269|PubMed:20488895}.
CC -!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
CC oxidoreductase family. {ECO:0000305}.
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DR EMBL; AF228637; AAF37698.1; -; mRNA.
DR EMBL; AB026636; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002686; AEE75887.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75888.1; -; Genomic_DNA.
DR EMBL; AY050376; AAK91394.1; -; mRNA.
DR EMBL; AY120695; AAM52238.1; -; mRNA.
DR EMBL; AK317007; BAH19701.1; -; mRNA.
DR RefSeq; NP_001078165.1; NM_001084696.1. [A8MS68-1]
DR RefSeq; NP_566562.1; NM_112571.3. [A8MS68-2]
DR AlphaFoldDB; A8MS68; -.
DR SMR; A8MS68; -.
DR BioGRID; 6284; 4.
DR IntAct; A8MS68; 1.
DR STRING; 3702.AT3G16950.2; -.
DR PaxDb; A8MS68; -.
DR PRIDE; A8MS68; -.
DR ProteomicsDB; 234923; -. [A8MS68-1]
DR EnsemblPlants; AT3G16950.1; AT3G16950.1; AT3G16950. [A8MS68-2]
DR EnsemblPlants; AT3G16950.2; AT3G16950.2; AT3G16950. [A8MS68-1]
DR GeneID; 820951; -.
DR Gramene; AT3G16950.1; AT3G16950.1; AT3G16950. [A8MS68-2]
DR Gramene; AT3G16950.2; AT3G16950.2; AT3G16950. [A8MS68-1]
DR KEGG; ath:AT3G16950; -.
DR Araport; AT3G16950; -.
DR TAIR; locus:2086177; AT3G16950.
DR eggNOG; KOG1335; Eukaryota.
DR HOGENOM; CLU_016755_0_1_1; -.
DR OMA; GTCINWG; -.
DR OrthoDB; 581771at2759; -.
DR PhylomeDB; A8MS68; -.
DR PRO; PR:A8MS68; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; A8MS68; baseline and differential.
DR Genevisible; A8MS68; AT.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; ISS:TAIR.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IBA:GO_Central.
DR GO; GO:0006086; P:acetyl-CoA biosynthetic process from pyruvate; TAS:TAIR.
DR GO; GO:0045454; P:cell redox homeostasis; IEA:InterPro.
DR GO; GO:0046685; P:response to arsenic-containing substance; IMP:UniProtKB.
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; 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 SUPFAM; SSF51905; SSF51905; 1.
DR SUPFAM; SSF55424; SSF55424; 1.
DR TIGRFAMs; TIGR01350; lipoamide_DH; 1.
DR PROSITE; PS00076; PYRIDINE_REDOX_1; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chloroplast; Disulfide bond; FAD; Flavoprotein; NAD;
KW Oxidoreductase; Plastid; Redox-active center; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..70
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 71..623
FT /note="Dihydrolipoyl dehydrogenase 1, chloroplastic"
FT /id="PRO_0000423493"
FT REGION 561..597
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 561..595
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 539
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 116..124
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 133
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 199
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 224..226
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 261..268
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 284
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 357
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 403
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 409..412
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT DISULFID 124..129
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT VAR_SEQ 564..570
FT /note="GDAKIKL -> VSEKVVV (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11056213,
FT ECO:0000303|PubMed:14593172"
FT /id="VSP_047927"
FT VAR_SEQ 571..623
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11056213,
FT ECO:0000303|PubMed:14593172"
FT /id="VSP_047928"
FT CONFLICT 14
FT /note="F -> L (in Ref. 5; BAH19701)"
FT /evidence="ECO:0000305"
FT CONFLICT 222
FT /note="I -> T (in Ref. 5; BAH19701)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 623 AA; 66661 MW; 6747C79E1D2DE365 CRC64;
MQSAMALSFS QTSFTRPNHV LGSSGSVFST PRSLRFCGLR REAFGFSTSN QLAIRSNRIQ
FLSRKSFQVS ASASSNGNGA PPKSFDYDLI IIGAGVGGHG AALHAVEKGL KTAIIEGDVV
GGTCVNRGCV PSKALLAVSG RMRELQNEHH MKSFGLQVSA AGYDRQGVAD HANNLATKIR
NNLTNSMKAI GVDILTGFGS VLGPQKVKYG KDNIITAKDI IIATGSVPFV PKGIEVDGKT
VITSDHALKL ESVPEWIAIV GSGYIGLEFS DVYTALGSEV TFIEALDQLM PGFDPEISKL
AQRVLINPRK IDYHTGVFAS KITPARDGKP VLIELIDAKT KEPKDTLEVD AALIATGRAP
FTNGLGLENV NVVTQRGFIP VDERMRVIDG KGTLVPNLYC IGDANGKLML AHAASAQGIS
VVEQVSGRDH VLNHLSIPAA CFTHPEISMV GLTEPQAKEK GEKEGFKVSV VKTSFKANTK
ALAENEGEGI AKMIYRPDNG EILGVHIFGL HAADLIHEAS NAIALGTRIQ DIKLAVHAHP
TLSEVLDELF KAAKVESHAT TRTGDAKIKL NTNQEDRKGR RRGGDDEKQP SVSKDLKDIS
TRPSSFFENI SVGVLSLLSL IFV
