Q9M5K2 (DLDH2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Dihydrolipoyl dehydrogenase 2, mitochondrial
Short name=AtmLPD2
Short name=mtLPD2
EC=1.8.1.4

Alternative name(s):
Dihydrolipoamide dehydrogenase 2
Glycine cleavage system L protein 2
Pyruvate dehydrogenase complex E3 subunit 2
Short name=E3-2
Short name=PDC-E3 2

Gene names

Name:	LPD2
Ordered Locus Names:	At3g17240
ORF Names:	MGD8.7

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › 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 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. Ref.1 Ref.10
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. 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).
Subcellular location	Mitochondrion matrix.
Tissue specificity	Preferentially expressed in roots, flowers and siliques and at a lower level in stems and leaves. Ref.1
Post-translational modification	S-nytrosylated at unknown positions.
Disruption phenotype	No visible phenotype, probably due to redundancy with LPD1.
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
Coding sequence diversity	Alternative splicing
Domain	Redox-active center Transit peptide
Ligand	FAD Flavoprotein NAD
Molecular function	Oxidoreductase
PTM	Disulfide bond S-nitrosylation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell redox homeostasis Inferred from electronic annotation. Source: InterPro response to cadmium ion Inferred from expression pattern PubMed 16502469. Source: TAIR
Cellular_component	apoplast Inferred from direct assay PubMed 21798377. Source: TAIR chloroplast Inferred from direct assay PubMed 15028209. Source: TAIR mitochondrial matrix Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrial respiratory chain complex I Inferred from direct assay PubMed 20197505. Source: TAIR
Molecular_function	ATP binding Inferred from direct assay PubMed 17137349. Source: TAIR cobalt ion binding Inferred from direct assay PubMed 20018591. Source: TAIR copper ion binding Inferred from direct assay PubMed 20018591. Source: TAIR dihydrolipoyl dehydrogenase activity Inferred from mutant phenotype Ref.1. Source: TAIR flavin adenine dinucleotide binding Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from direct assay PubMed 20018591. Source: TAIR
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9M5K2-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q9M5K2-2)

The sequence of this isoform differs from the canonical sequence as follows:
     92-127: ALLHSSHMYHEAKHVFANHGVKVSSVEVDLPAMLAQ → VILETPFPITLIRRKFSPIFIRLLWNLLVDHHLDSI
     128-507: Missing.

Note: May be due to an intron retention. No experimental confirmation available.

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 2, mitochondrial		PRO_0000260230
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
	Modified residue	372	1	S-nitrosocysteine
	Disulfide bond	82 ↔ 87		Redox-active By similarity
Natural variations
	Alternative sequence	92 – 127	36	ALLHS…AMLAQ → VILETPFPITLIRRKFSPIF IRLLWNLLVDHHLDSI in isoform 2.		VSP_021588
	Alternative sequence	128 – 507	380	Missing in isoform 2.		VSP_021589

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: C5CA38074A8103D7	FASTA	507	53,986
	10 20 30 40 50 60 MAMASLARRK AYFLTRNISN SPTDAFRFSF SLTRGFASSG SDDNDVVIIG GGPGGYVAAI 70 80 90 100 110 120 KAAQLGLKTT CIEKRGALGG TCLNVGCIPS KALLHSSHMY HEAKHVFANH GVKVSSVEVD 130 140 150 160 170 180 LPAMLAQKDT AVKNLTRGVE GLFKKNKVNY VKGYGKFLSP SEVSVDTIDG ENVVVKGKHI 190 200 210 220 230 240 IVATGSDVKS LPGITIDEKK IVSSTGALSL TEIPKKLIVI GAGYIGLEMG SVWGRLGSEV 250 260 270 280 290 300 TVVEFAADIV PAMDGEIRKQ FQRSLEKQKM KFMLKTKVVG VDSSGDGVKL IVEPAEGGEQ 310 320 330 340 350 360 TTLEADVVLV SAGRTPFTSG LDLEKIGVET DKGGRILVNE RFSTNVSGVY AIGDVIPGPM 370 380 390 400 410 420 LAHKAEEDGV ACVEFIAGKH GHVDYDKVPG VVYTYPEVAS VGKTEEQLKK EGVSYNVGKF 430 440 450 460 470 480 PFMANSRAKA IDTAEGMVKI LADKETDKIL GVHIMSPNAG ELIHEAVLAI NYDASSEDIA 490 500 RVCHAHPTMS EAIKEAAMAT YDKPIHM
	Isoform 2 [UniParc]. Checksum: 54FBD724E3ED97E3	FASTA	127	13,729
	10 20 30 40 50 60 MAMASLARRK AYFLTRNISN SPTDAFRFSF SLTRGFASSG SDDNDVVIIG GGPGGYVAAI 70 80 90 100 110 120 KAAQLGLKTT CIEKRGALGG TCLNVGCIPS KVILETPFPI TLIRRKFSPI FIRLLWNLLV DHHLDSI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of two cDNAs encoding mitochondrial lipoamide dehydrogenase from Arabidopsis." Lutziger I., Oliver D.J. Plant Physiol. 127:615-623(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones." Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S. DNA Res. 7:131-135(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Arabidopsis ORF clones." Shinn P., Chen H., Kim C.J., Ecker J.R. Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: cv. Columbia.
[5]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[6]	"Cloning and characterization of 2-oxoglutarate dehydrogenase from Arabidopsis thaliana." Machuy N., Klein M., Mueller-Roeber B. Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 36-507 (ISOFORM 1). Strain: cv. Columbia.
[7]	"The glycine decarboxylase system: a fascinating complex." Douce R., Bourguignon J., Neuburger M., Rebeille F. Trends Plant Sci. 6:167-176(2001) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[8]	"Genetic manipulation of glycine decarboxylation." Bauwe H., Kolukisaoglu U. J. Exp. Bot. 54:1523-1535(2003) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW, NOMENCLATURE.
[9]	"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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS]. Strain: cv. Landsberg erecta.
[10]	"Lipoic acid-dependent oxidative catabolism of alpha-keto acids in mitochondria provides evidence for branched-chain amino acid catabolism in Arabidopsis." Taylor N.L., Heazlewood J.L., Day D.A., Millar A.H. Plant Physiol. 134:838-848(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"Regulation of plant glycine decarboxylase by s-nitrosylation and glutathionylation." Palmieri M.C., Lindermayr C., Bauwe H., Steinhauser C., Durner J. Plant Physiol. 152:1514-1528(2010) [PubMed] [Europe PMC] [Abstract] Cited for: S-NITROSYLATION.
[12]	"Proteomics investigation of endogenous S-nitrosylation in Arabidopsis." Fares A., Rossignol M., Peltier J.B. Biochem. Biophys. Res. Commun. 416:331-336(2011) [PubMed] [Europe PMC] [Abstract] Cited for: S-NITROSYLATION AT CYS-372.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF228640 mRNA. Translation: AAF34796.1. AB022216 Genomic DNA. No translation available. CP002686 Genomic DNA. Translation: AEE75925.1. CP002686 Genomic DNA. Translation: AEE75926.1. CP002686 Genomic DNA. Translation: AEE75927.1. BT024578 mRNA. Translation: ABD38917.1. AY087203 mRNA. Translation: AAM64759.1. AJ223804 mRNA. Translation: CAA11554.1.
IPI	IPI00519283. IPI00522612.
RefSeq	NP_566570.3. NM_112601.3. NP_566571.1. NM_112602.1. NP_851005.1. NM_180674.3.
UniGene	At.20793.
3D structure databases
HSSP	HSSP built from PDB template 1DXL based on UniProtKB P31023.
ProteinModelPortal	Q9M5K2.
SMR	Q9M5K2. Positions 41-507.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9M5K2. 1 interaction.
STRING	3702.AT3G17240.3-P.
Proteomic databases
PaxDb	Q9M5K2.
PRIDE	Q9M5K2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT3G17240.1; AT3G17240.1; AT3G17240. AT3G17240.3; AT3G17240.3; AT3G17240.
GeneID	820984.
KEGG	ath:AT3G17240.
Organism-specific databases
GeneFarm	4375. 442.
TAIR	At3g17240.
Phylogenomic databases
eggNOG	COG1249.
HOGENOM	HOG000276708.
InParanoid	Q9M5K2.
KO	K00382.
OMA	TIMEAEL.
PhylomeDB	Q9M5K2.
ProtClustDB	CLSN2682168.
Gene expression databases
Genevestigator	Q9M5K2.
GermOnline	AT3G17240. Arabidopsis thaliana.
Family and domain databases
Gene3D	3.30.390.30. 1 hit.
InterPro	IPR016156. FAD/NAD-linked_Rdtase_dimer. IPR013027. FAD_pyr_nucl-diS_OxRdtase. IPR006258. Lipoamide_DH. IPR004099. Pyr_nucl-diS_OxRdtase_dimer. IPR023753. Pyr_nucl-diS_OxRdtase_FAD/NAD. IPR012999. Pyr_OxRdtase_I_AS. IPR001327. Pyr_OxRdtase_NAD-bd_dom. [Graphical view]
PANTHER	PTHR22912:SF20. PTHR22912:SF20. 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.
SUPFAM	SSF55424. FAD/NAD-linked_reductase_dimer. 1 hit.
TIGRFAMs	TIGR01350. lipoamide_DH. 1 hit.
PROSITE	PS00076. PYRIDINE_REDOX_1. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DLDH2_ARATH

Accession

Primary (citable) accession number: Q9M5K2
Secondary accession number(s): Q8LBH6, Q9ZRQ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 28, 2006
Last sequence update:	October 1, 2000
Last modified:	May 1, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program