DLDH1_ARATH
ID DLDH1_ARATH Reviewed; 507 AA.
AC Q9M5K3; Q9LNF3;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 2.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=Dihydrolipoyl dehydrogenase 1, mitochondrial;
DE Short=AtmLPD1;
DE Short=mtLPD1;
DE EC=1.8.1.4;
DE AltName: Full=Dihydrolipoamide dehydrogenase 1;
DE AltName: Full=Glycine cleavage system L protein 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=At1g48030; ORFNames=F21D18.28, T2J15.6;
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], FUNCTION, TISSUE SPECIFICITY, AND INDUCTION BY
RP LIGHT.
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 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 [5]
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 [6]
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 [7]
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 [8]
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).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP PHE-36.
RX PubMed=25862457; DOI=10.1104/pp.15.00300;
RA Huang S., Nelson C.J., Li L., Taylor N.L., Stroeher E., Peteriet J.,
RA Millar A.H.;
RT "INTERMEDIATE CLEAVAGE PEPTIDASE55 modifies enzyme amino termini and alters
RT protein stability in Arabidopsis mitochondria.";
RL Plant Physiol. 168:415-427(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}.
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 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:0000305|PubMed:25732537,
CC ECO:0000305|PubMed:25862457}.
CC -!- TISSUE SPECIFICITY: Preferentially expressed in leaves, flowers and
CC siliques and at a lower level in roots and stems.
CC {ECO:0000269|PubMed:11598235}.
CC -!- INDUCTION: Up-regulated by light. {ECO:0000269|PubMed:11598235}.
CC -!- PTM: S-nytrosylated at unknown positions.
CC -!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
CC -!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
CC oxidoreductase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF79529.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF228639; AAF34795.3; -; mRNA.
DR EMBL; AC023673; AAF79529.1; ALT_INIT; Genomic_DNA.
DR EMBL; AC051631; AAG51522.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32239.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32240.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59707.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59708.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59709.1; -; Genomic_DNA.
DR PIR; F96520; F96520.
DR RefSeq; NP_001322047.1; NM_001333291.1.
DR RefSeq; NP_001322048.1; NM_001333289.1.
DR RefSeq; NP_001322049.1; NM_001333290.1.
DR RefSeq; NP_175237.1; NM_103699.5.
DR RefSeq; NP_849782.1; NM_179451.1.
DR AlphaFoldDB; Q9M5K3; -.
DR SMR; Q9M5K3; -.
DR BioGRID; 26446; 8.
DR IntAct; Q9M5K3; 1.
DR STRING; 3702.AT1G48030.2; -.
DR iPTMnet; Q9M5K3; -.
DR MetOSite; Q9M5K3; -.
DR PaxDb; Q9M5K3; -.
DR PRIDE; Q9M5K3; -.
DR ProteomicsDB; 222209; -.
DR EnsemblPlants; AT1G48030.1; AT1G48030.1; AT1G48030.
DR EnsemblPlants; AT1G48030.2; AT1G48030.2; AT1G48030.
DR EnsemblPlants; AT1G48030.3; AT1G48030.3; AT1G48030.
DR EnsemblPlants; AT1G48030.4; AT1G48030.4; AT1G48030.
DR EnsemblPlants; AT1G48030.5; AT1G48030.5; AT1G48030.
DR GeneID; 841221; -.
DR Gramene; AT1G48030.1; AT1G48030.1; AT1G48030.
DR Gramene; AT1G48030.2; AT1G48030.2; AT1G48030.
DR Gramene; AT1G48030.3; AT1G48030.3; AT1G48030.
DR Gramene; AT1G48030.4; AT1G48030.4; AT1G48030.
DR Gramene; AT1G48030.5; AT1G48030.5; AT1G48030.
DR KEGG; ath:AT1G48030; -.
DR Araport; AT1G48030; -.
DR TAIR; locus:2023782; AT1G48030.
DR eggNOG; KOG1335; Eukaryota.
DR HOGENOM; CLU_016755_0_1_1; -.
DR InParanoid; Q9M5K3; -.
DR OMA; DAKYGEW; -.
DR OrthoDB; 581771at2759; -.
DR PhylomeDB; Q9M5K3; -.
DR BioCyc; ARA:AT1G48030-MON; -.
DR BRENDA; 1.4.1.27; 399.
DR PRO; PR:Q9M5K3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9M5K3; baseline and differential.
DR Genevisible; Q9M5K3; AT.
DR GO; GO:0048046; C:apoplast; 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; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; HDA: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; IBA:GO_Central.
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 GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
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 Disulfide bond; FAD; Flavoprotein; Mitochondrion; NAD; Oxidoreductase;
KW Redox-active center; Reference proteome; Transit peptide.
FT TRANSIT 1..36
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537,
FT ECO:0000269|PubMed:25862457"
FT CHAIN 37..507
FT /note="Dihydrolipoyl dehydrogenase 1, mitochondrial"
FT /id="PRO_0000260229"
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"
SQ SEQUENCE 507 AA; 53988 MW; 10AB577E04164B89 CRC64;
MAMASLARRK AYFLTRNLSN SPTDALRFSF SLSRGFASSG SDENDVVIIG GGPGGYVAAI
KASQLGLKTT CIEKRGALGG TCLNVGCIPS KALLHSSHMY HEAKHSFANH GIKVSSVEVD
LPAMLAQKDN AVKNLTRGIE GLFKKNKVTY VKGYGKFISP NEVSVETIDG GNTIVKGKHI
IVATGSDVKS LPGITIDEKK IVSSTGALSL SEVPKKLIVI GAGYIGLEMG SVWGRLGSEV
TVVEFAGDIV PSMDGEIRKQ FQRSLEKQKM KFMLKTKVVS VDSSSDGVKL TVEPAEGGEQ
SILEADVVLV SAGRTPFTSG LDLEKIGVET DKAGRILVND RFLSNVPGVY AIGDVIPGPM
LAHKAEEDGV ACVEFIAGKH GHVDYDKVPG VVYTHPEVAS VGKTEEQLKK EGVSYRVGKF
PFMANSRAKA IDNAEGLVKI LADKETDKIL GVHIMAPNAG ELIHEAVLAI NYDASSEDIA
RVCHAHPTMS EALKEAAMAT YDKPIHI
