PLPD2_ARATH
ID PLPD2_ARATH Reviewed; 567 AA.
AC F4JLP5; Q9M5K4;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 18-SEP-2013, sequence version 2.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=Dihydrolipoyl dehydrogenase 2, chloroplastic;
DE Short=ptLPD2;
DE EC=1.8.1.4;
DE AltName: Full=Dihydrolipoamide dehydrogenase 2;
DE AltName: Full=Protein LIPOAMIDE DEHYDROGENASE 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=At4g16155; ORFNames=FCAALL.61;
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], FUNCTION, AND 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=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [4]
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]
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 {ECO:0000250}.
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; AF228638; AAF37699.1; -; mRNA.
DR EMBL; Z97340; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AL161543; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002687; AEE83704.2; -; Genomic_DNA.
DR EMBL; AY050877; AAK92814.1; -; mRNA.
DR EMBL; AY054195; AAL06856.1; -; mRNA.
DR EMBL; AY113958; AAM45006.1; -; mRNA.
DR RefSeq; NP_567487.5; NM_117711.8.
DR AlphaFoldDB; F4JLP5; -.
DR SMR; F4JLP5; -.
DR BioGRID; 12601; 4.
DR STRING; 3702.AT4G16155.1; -.
DR MetOSite; F4JLP5; -.
DR PaxDb; F4JLP5; -.
DR PRIDE; F4JLP5; -.
DR ProteomicsDB; 226203; -.
DR EnsemblPlants; AT4G16155.1; AT4G16155.1; AT4G16155.
DR GeneID; 827307; -.
DR Gramene; AT4G16155.1; AT4G16155.1; AT4G16155.
DR KEGG; ath:AT4G16155; -.
DR Araport; AT4G16155; -.
DR TAIR; locus:505006477; AT4G16155.
DR eggNOG; KOG1335; Eukaryota.
DR HOGENOM; CLU_016755_0_1_1; -.
DR InParanoid; F4JLP5; -.
DR OMA; WASMLND; -.
DR OrthoDB; 581771at2759; -.
DR PhylomeDB; F4JLP5; -.
DR PRO; PR:F4JLP5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JLP5; baseline and differential.
DR Genevisible; F4JLP5; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IBA:GO_Central.
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; 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 PROSITE; PS00076; PYRIDINE_REDOX_1; 1.
PE 2: Evidence at transcript level;
KW Chloroplast; Disulfide bond; FAD; Flavoprotein; NAD; Oxidoreductase;
KW Plastid; Redox-active center; Reference proteome; Transit peptide.
FT TRANSIT 1..67
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 68..567
FT /note="Dihydrolipoyl dehydrogenase 2, chloroplastic"
FT /id="PRO_0000423494"
FT ACT_SITE 536
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 114..122
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 131
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 197
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 221..223
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 258..265
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 281
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 354
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 400
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 406..409
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT DISULFID 122..127
FT /note="Redox-active"
FT /evidence="ECO:0000250"
SQ SEQUENCE 567 AA; 60145 MW; BAC2D3EE9BB4D250 CRC64;
MQSVLSLSFS QASLPLANRT LCSSNAAPST PRNLRFCGLR REAFCFSPSK QLTSCRFHIQ
SRRIEVSAAA SSSAGNGAPS KSFDYDLIII GAGVGGHGAA LHAVEKGLKT AIIEGDVVGG
TCVNRGCVPS KALLAVSGRM RELQNEHHMK AFGLQVSAAG YDRQGVADHA SNLATKIRNN
LTNSMKALGV DILTGFGAVL GPQKVKYGDN IITGKDIIIA TGSVPFVPKG IEVDGKTVIT
SDHALKLESV PDWIAIVGSG YIGLEFSDVY TALGSEVTFI EALDQLMPGF DPEISKLAQR
VLINTRKIDY HTGVFASKIT PAKDGKPVLI ELIDAKTKEP KDTLEVDAAL IATGRAPFTN
GLGLENINVT TQRGFIPVDE RMRVIDGNGK LVPHLYCIGD ANGKLMLAHA ASAQGISVVE
QVTGRDHVLN HLSIPAACFT HPEISMVGLT EPQAREKAEK EGFKVSIAKT SFKANTKALA
ENEGEGLAKM IYRPDNGEIL GVHIFGLHAA DLIHEASNAI ALGTRIQDIK LAVHAHPTLS
EVVDELFKAA KVDSPASVTA QSVKVTV
