Reviewed, UniProtKB/Swiss-Prot Q9M5K3 (DLDH1_ARATH)

Names and origin

Protein names

Recommended name:
    Dihydrolipoyl dehydrogenase 1, mitochondrial
    EC=1.8.1.4
Alternative name(s):
    Dihydrolipoamide dehydrogenase 1
    Pyruvate dehydrogenase complex E3 subunit 1
      Short name=PDC-E3 1
      Short name=E3-1
    Glycine cleavage system L protein 1

Gene names

Name:	LPD1
Ordered Locus Names:	At1g48030
ORF Names:	F21D18.28, T2J15.6

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	507 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. The pyruvate dehydrogenase complex contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). Ref.1
Catalytic activity	Protein N(6)-(dihydrolipoyl)lysine + NAD+ = protein N(6)-(lipoyl)lysine + NADH.
Cofactor	Binds 1 FAD per subunit By similarity.
Subunit structure	Homodimer By similarity.
Subcellular location	Mitochondrion matrix. Ref.3
Tissue specificity	Preferentially expressed in leaves, flowers and siliques and at a lower level in roots and stems. Ref.1
Miscellaneous	The active site is a redox-active disulfide bond.
Sequence similarities	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.

Ontologies

Keywords
Cellular component	Mitochondrion
Domain	Redox-active center Transit peptide
Ligand	FAD Flavoprotein NAD
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	cell redox homeostasis Inferred from electronic annotation. Source: InterPro oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW response to cadmium ion Inferred from expression pattern. Source: TAIR
Cellular component	apoplast Inferred from direct assay. Source: TAIR mitochondrial matrix Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from direct assay. Source: TAIR FAD binding Inferred from electronic annotation. Source: InterPro dihydrolipoyl dehydrogenase activity Inferred from electronic annotation. Source: EC protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
TRX3	Q42403	1	EBI-449547,EBI-449157

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 36	36	Mitochondrion Potential
	Chain	37 – 507	471	Dihydrolipoyl dehydrogenase 1, mitochondrial		PRO_0000260229
Regions
	Nucleotide binding	73 – 82	10	FAD By similarity
	Nucleotide binding	184 – 186	3	FAD By similarity
	Nucleotide binding	221 – 228	8	NAD By similarity
	Nucleotide binding	360 – 363	4	FAD By similarity
Sites
	Active site	486	1	Proton acceptor By similarity
	Binding site	91	1	FAD By similarity
	Binding site	155	1	FAD; via amide nitrogen and carbonyl oxygen By similarity
	Binding site	244	1	NAD By similarity
	Binding site	278	1	NAD; via amide nitrogen and carbonyl oxygen By similarity
	Binding site	313	1	NAD; via amide nitrogen By similarity
	Binding site	354	1	FAD By similarity
Amino acid modifications
	Disulfide bond	82 ↔ 87		Redox-active By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9M5K3-1 [UniParc]. Last modified June 1, 2001. Version 2. Checksum: 10AB577E04164B89	FASTA	507	53,988
	10 20 30 40 50 60 MAMASLARRK AYFLTRNLSN SPTDALRFSF SLSRGFASSG SDENDVVIIG GGPGGYVAAI 70 80 90 100 110 120 KASQLGLKTT CIEKRGALGG TCLNVGCIPS KALLHSSHMY HEAKHSFANH GIKVSSVEVD 130 140 150 160 170 180 LPAMLAQKDN AVKNLTRGIE GLFKKNKVTY VKGYGKFISP NEVSVETIDG GNTIVKGKHI 190 200 210 220 230 240 IVATGSDVKS LPGITIDEKK IVSSTGALSL SEVPKKLIVI GAGYIGLEMG SVWGRLGSEV 250 260 270 280 290 300 TVVEFAGDIV PSMDGEIRKQ FQRSLEKQKM KFMLKTKVVS VDSSSDGVKL TVEPAEGGEQ 310 320 330 340 350 360 SILEADVVLV SAGRTPFTSG LDLEKIGVET DKAGRILVND RFLSNVPGVY AIGDVIPGPM 370 380 390 400 410 420 LAHKAEEDGV ACVEFIAGKH GHVDYDKVPG VVYTHPEVAS VGKTEEQLKK EGVSYRVGKF 430 440 450 460 470 480 PFMANSRAKA IDNAEGLVKI LADKETDKIL GVHIMAPNAG ELIHEAVLAI NYDASSEDIA 490 500 RVCHAHPTMS EALKEAAMAT YDKPIHI

References

[1]	"Characterization of two cDNAs encoding mitochondrial lipoamide dehydrogenase from Arabidopsis." Lutziger I., Oliver D.J. Plant Physiol. 127:615-623(2001) [PubMed: 11598235] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." 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. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	"Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins." Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J., Millar A.H. Plant Cell 16:241-256(2004) [PubMed: 14671022] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF228639 mRNA. Translation: AAF34795.3. AC023673 Genomic DNA. Translation: AAF79529.1. Different initiation. AC051631 Genomic DNA. Translation: AAG51522.1.
IPI	IPI00532806.
PIR	F96520.
RefSeq	NP_175237.1. NP_849782.1.
UniGene	At.15211
3D structure databases
HSSP	HSSP built from PDB template 1DXL based on UniProtKB P31023.
SMR	Q9M5K3. Positions 41-507.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9M5K3. 1 interaction.
Proteomic databases
PRIDE	Q9M5K3.
ProMEX	Q9M5K3.
Genome annotation databases
GeneID	841221.
GenomeReviews	Gene locus AT1G48030 in contig CT485782_GR.
KEGG	ath:AT1G48030.
NMPDR	fig|3702.1.peg.4264.
Organism-specific databases
GeneFarm	4374. 442.
TAIR	At1g48030.
Phylogenomic databases
OMA	Q9M5K3. YLERICP.
Enzyme and pathway databases
BRENDA	1.8.1.4. 302.
Gene expression databases
GermOnline	AT1G48030. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR013027. FAD_pyr_nucl-diS_OxRdtase. IPR000815. Hg_reductase. IPR006258. Lipoamide_DH. IPR004099. Pyr_nucl-diS_OxRdtase_dimer. IPR012999. Pyr_OxRdtase_I_AS. IPR001327. Pyr_OxRdtase_NAD_bd. [Graphical view]
Gene3D	G3DSA:3.30.390.30. Pyr_redox_dim. 1 hit.
PANTHER	PTHR22912:SF20. Lipoamide_DH. 1 hit.
Pfam	PF00070. Pyr_redox. 1 hit. PF07992. Pyr_redox_2. 1 hit. PF02852. Pyr_redox_dim. 1 hit. [Graphical view]
PRINTS	PR00368. FADPNR. PR00945. HGRDTASE.
ProDom	PD000139. FAD_pyr_redox. 1 hit. [Graphical view] [Entries sharing at least one domain]
TIGRFAMs	TIGR01350. lipoamide_DH. 1 hit.
PROSITE	PS00076. PYRIDINE_REDOX_1. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DLDH1_ARATH

Accession

Primary (citable) accession number: Q9M5K3
Secondary accession number(s): Q9LNF3

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 28, 2006
Last sequence update:	June 1, 2001
Last modified:	June 16, 2009
This is version 59 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)