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Dihydrolipoyl dehydrogenase 1, mitochondrial (AtmLPD1) (mtLPD1) (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase 1) (Glycine cleavage system L protein 1) (Pyruvate dehydrogenase complex E3 subunit 1) (E3-1) (PDC-E3 1)

 DLDH1_ARATH             Reviewed;         507 AA.
Q9M5K3; Q9LNF3;
28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
01-JUN-2001, sequence version 2.
22-NOV-2017, entry version 133.
RecName: Full=Dihydrolipoyl dehydrogenase 1, mitochondrial;
Short=AtmLPD1;
Short=mtLPD1;
EC=1.8.1.4;
AltName: Full=Dihydrolipoamide dehydrogenase 1;
AltName: Full=Glycine cleavage system L protein 1;
AltName: Full=Pyruvate dehydrogenase complex E3 subunit 1;
Short=E3-1;
Short=PDC-E3 1;
Flags: Precursor;
Name=LPD1; OrderedLocusNames=At1g48030; ORFNames=F21D18.28, T2J15.6;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND
INDUCTION BY LIGHT.
PubMed=11598235; DOI=10.1104/pp.127.2.615;
Lutziger I., Oliver D.J.;
"Characterization of two cDNAs encoding mitochondrial lipoamide
dehydrogenase from Arabidopsis.";
Plant Physiol. 127:615-623(2001).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[4]
REVIEW.
PubMed=11286922; DOI=10.1016/S1360-1385(01)01892-1;
Douce R., Bourguignon J., Neuburger M., Rebeille F.;
"The glycine decarboxylase system: a fascinating complex.";
Trends Plant Sci. 6:167-176(2001).
[5]
REVIEW, AND NOMENCLATURE.
PubMed=12730263; DOI=10.1093/jxb/erg171;
Bauwe H., Kolukisaoglu U.;
"Genetic manipulation of glycine decarboxylation.";
J. Exp. Bot. 54:1523-1535(2003).
[6]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE
SCALE ANALYSIS].
STRAIN=cv. Landsberg erecta;
PubMed=14671022; DOI=10.1105/tpc.016055;
Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
Millar A.H.;
"Experimental analysis of the Arabidopsis mitochondrial proteome
highlights signaling and regulatory components, provides assessment of
targeting prediction programs, and indicates plant-specific
mitochondrial proteins.";
Plant Cell 16:241-256(2004).
[7]
S-NITROSYLATION.
PubMed=20089767; DOI=10.1104/pp.109.152579;
Palmieri M.C., Lindermayr C., Bauwe H., Steinhauser C., Durner J.;
"Regulation of plant glycine decarboxylase by s-nitrosylation and
glutathionylation.";
Plant Physiol. 152:1514-1528(2010).
[8]
IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE
AFTER PHE-36.
PubMed=25732537; DOI=10.1093/jxb/erv064;
Carrie C., Venne A.S., Zahedi R.P., Soll J.;
"Identification of cleavage sites and substrate proteins for two
mitochondrial intermediate peptidases in Arabidopsis thaliana.";
J. Exp. Bot. 66:2691-2708(2015).
[9]
IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE
AFTER PHE-36.
PubMed=25862457; DOI=10.1104/pp.15.00300;
Huang S., Nelson C.J., Li L., Taylor N.L., Stroeher E., Peteriet J.,
Millar A.H.;
"INTERMEDIATE CLEAVAGE PEPTIDASE55 modifies enzyme amino termini and
alters protein stability in Arabidopsis mitochondria.";
Plant Physiol. 168:415-427(2015).
-!- FUNCTION: Lipoamide dehydrogenase is a component of the glycine
decarboxylase (GDC) or glycine cleavage system as well as of the
alpha-ketoacid dehydrogenase complexes. LPD1 is probably the
protein most often associated with the glycine decarboxylase
complex while LPD2 is probably incorporated into alpha-ketoacid
dehydrogenase complexes. {ECO:0000269|PubMed:11598235}.
-!- CATALYTIC ACTIVITY: Protein N(6)-(dihydrolipoyl)lysine + NAD(+) =
protein N(6)-(lipoyl)lysine + NADH.
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
Note=Binds 1 FAD per subunit. {ECO:0000250};
-!- SUBUNIT: Homodimer (By similarity). Part of both the glycine
cleavage system composed of four proteins: P, T, L and H and of
the pyruvate dehydrogenase complex containing multiple copies of
three enzymatic components: pyruvate dehydrogenase (E1),
dihydrolipoamide acetyltransferase (E2) and lipoamide
dehydrogenase (E3). {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Mitochondrion matrix
{ECO:0000269|PubMed:14671022, ECO:0000305|PubMed:25732537,
ECO:0000305|PubMed:25862457}.
-!- TISSUE SPECIFICITY: Preferentially expressed in leaves, flowers
and siliques and at a lower level in roots and stems.
{ECO:0000269|PubMed:11598235}.
-!- INDUCTION: Up-regulated by light. {ECO:0000269|PubMed:11598235}.
-!- PTM: S-nytrosylated at unknown positions.
-!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
-!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
oxidoreductase family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAF79529.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AF228639; AAF34795.3; -; mRNA.
EMBL; AC023673; AAF79529.1; ALT_INIT; Genomic_DNA.
EMBL; AC051631; AAG51522.1; -; Genomic_DNA.
EMBL; CP002684; AEE32239.1; -; Genomic_DNA.
EMBL; CP002684; AEE32240.1; -; Genomic_DNA.
EMBL; CP002684; ANM59707.1; -; Genomic_DNA.
EMBL; CP002684; ANM59708.1; -; Genomic_DNA.
EMBL; CP002684; ANM59709.1; -; Genomic_DNA.
PIR; F96520; F96520.
RefSeq; NP_001322047.1; NM_001333291.1.
RefSeq; NP_001322048.1; NM_001333289.1.
RefSeq; NP_001322049.1; NM_001333290.1.
RefSeq; NP_175237.1; NM_103699.5.
RefSeq; NP_849782.1; NM_179451.1.
UniGene; At.15211; -.
ProteinModelPortal; Q9M5K3; -.
SMR; Q9M5K3; -.
BioGrid; 26446; 2.
IntAct; Q9M5K3; 1.
STRING; 3702.AT1G48030.1; -.
iPTMnet; Q9M5K3; -.
PaxDb; Q9M5K3; -.
PRIDE; Q9M5K3; -.
EnsemblPlants; AT1G48030.1; AT1G48030.1; AT1G48030.
EnsemblPlants; AT1G48030.2; AT1G48030.2; AT1G48030.
EnsemblPlants; AT1G48030.3; AT1G48030.3; AT1G48030.
EnsemblPlants; AT1G48030.4; AT1G48030.4; AT1G48030.
EnsemblPlants; AT1G48030.5; AT1G48030.5; AT1G48030.
GeneID; 841221; -.
Gramene; AT1G48030.1; AT1G48030.1; AT1G48030.
Gramene; AT1G48030.2; AT1G48030.2; AT1G48030.
Gramene; AT1G48030.3; AT1G48030.3; AT1G48030.
Gramene; AT1G48030.4; AT1G48030.4; AT1G48030.
Gramene; AT1G48030.5; AT1G48030.5; AT1G48030.
KEGG; ath:AT1G48030; -.
Araport; AT1G48030; -.
TAIR; locus:2023782; AT1G48030.
eggNOG; KOG1335; Eukaryota.
eggNOG; COG1249; LUCA.
HOGENOM; HOG000276708; -.
InParanoid; Q9M5K3; -.
KO; K00382; -.
OMA; CIDEWKN; -.
OrthoDB; EOG09360892; -.
PhylomeDB; Q9M5K3; -.
BioCyc; ARA:AT1G48030-MONOMER; -.
Reactome; R-ATH-204174; Regulation of pyruvate dehydrogenase (PDH) complex.
Reactome; R-ATH-5362517; Signaling by Retinoic Acid.
Reactome; R-ATH-6783984; Glycine degradation.
Reactome; R-ATH-70268; Pyruvate metabolism.
Reactome; R-ATH-70895; Branched-chain amino acid catabolism.
Reactome; R-ATH-71064; Lysine catabolism.
Reactome; R-ATH-71403; Citric acid cycle (TCA cycle).
PRO; PR:Q9M5K3; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; Q9M5K3; baseline and differential.
Genevisible; Q9M5K3; AT.
GO; GO:0048046; C:apoplast; IDA:TAIR.
GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
GO; GO:0005747; C:mitochondrial respiratory chain complex I; IDA:TAIR.
GO; GO:0005739; C:mitochondrion; IDA:TAIR.
GO; GO:0005524; F:ATP binding; IDA:TAIR.
GO; GO:0050897; F:cobalt ion binding; IDA:TAIR.
GO; GO:0005507; F:copper ion binding; IDA:TAIR.
GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IEA:UniProtKB-EC.
GO; GO:0009055; F:electron carrier activity; IEA:InterPro.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
GO; GO:0008270; F:zinc ion binding; IDA:TAIR.
GO; GO:0045454; P:cell redox homeostasis; IEA:InterPro.
GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
Gene3D; 3.30.390.30; -; 1.
Gene3D; 3.50.50.60; -; 1.
InterPro; IPR036188; FAD/NAD-bd_sf.
InterPro; IPR023753; FAD/NAD-binding_dom.
InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer_sf.
InterPro; IPR006258; Lipoamide_DH.
InterPro; IPR001100; Pyr_nuc-diS_OxRdtase.
InterPro; IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
InterPro; IPR012999; Pyr_OxRdtase_I_AS.
Pfam; PF07992; Pyr_redox_2; 1.
Pfam; PF02852; Pyr_redox_dim; 1.
PIRSF; PIRSF000350; Mercury_reductase_MerA; 1.
SUPFAM; SSF51905; SSF51905; 1.
SUPFAM; SSF55424; SSF55424; 1.
TIGRFAMs; TIGR01350; lipoamide_DH; 1.
PROSITE; PS00076; PYRIDINE_REDOX_1; 1.
1: Evidence at protein level;
Complete proteome; Disulfide bond; FAD; Flavoprotein; Mitochondrion;
NAD; Oxidoreductase; Redox-active center; Reference proteome;
Transit peptide.
TRANSIT 1 36 Mitochondrion.
{ECO:0000269|PubMed:25732537,
ECO:0000269|PubMed:25862457}.
CHAIN 37 507 Dihydrolipoyl dehydrogenase 1,
mitochondrial.
/FTId=PRO_0000260229.
NP_BIND 73 82 FAD. {ECO:0000250}.
NP_BIND 184 186 FAD. {ECO:0000250}.
NP_BIND 221 228 NAD. {ECO:0000250}.
NP_BIND 360 363 FAD. {ECO:0000250}.
ACT_SITE 486 486 Proton acceptor. {ECO:0000250}.
BINDING 91 91 FAD. {ECO:0000250}.
BINDING 155 155 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000250}.
BINDING 244 244 NAD. {ECO:0000250}.
BINDING 278 278 NAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000250}.
BINDING 313 313 NAD; via amide nitrogen. {ECO:0000250}.
BINDING 354 354 FAD. {ECO:0000250}.
DISULFID 82 87 Redox-active. {ECO:0000250}.
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


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