Dihydrolipoyl dehydrogenase 1, mitochondrial precursor - Arabidopsis thaliana (Mouse-ear cress)

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Q9M5K3 (DLDH1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 93. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Dihydrolipoyl dehydrogenase 1, mitochondrial
Short name=AtmLPD1
Short name=mtLPD1
EC=1.8.1.4

Alternative name(s):
Dihydrolipoamide dehydrogenase 1
Glycine cleavage system L protein 1
Pyruvate dehydrogenase complex E3 subunit 1
Short name=E3-1
Short name=PDC-E3 1

Gene names

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

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › 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
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 leaves, flowers and siliques and at a lower level in roots and stems. Ref.1
Induction	Up-regulated by light.
Post-translational modification	S-nytrosylated at unknown positions.
Miscellaneous	The active site is a redox-active disulfide bond.
Sequence similarities	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.
Sequence caution	The sequence AAF79529.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Cellular component	Mitochondrion
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 PubMed 20005002. Source: TAIR
Cellular_component	apoplast Inferred from direct assay PubMed 18538804. 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 electronic annotation. Source: EC flavin adenine dinucleotide binding Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from direct assay PubMed 20018591. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 36

Mitochondrion Potential

Chain

37 – 507

471

Dihydrolipoyl dehydrogenase 1, mitochondrial

PRO_0000260229

Regions

Nucleotide binding

73 – 82

FAD By similarity

Nucleotide binding

184 – 186

FAD By similarity

Nucleotide binding

221 – 228

NAD By similarity

Nucleotide binding

360 – 363

FAD By similarity

Sites

Active site

486

Proton acceptor By similarity

Binding site

FAD By similarity

Binding site

155

FAD; via amide nitrogen and carbonyl oxygen By similarity

Binding site

244

NAD By similarity

Binding site

278

NAD; via amide nitrogen and carbonyl oxygen By similarity

Binding site

313

NAD; via amide nitrogen By similarity

Binding site

354

FAD By similarity

Amino acid modifications

Disulfide bond

82 ↔ 87

Redox-active By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q9M5K3 [UniParc].

Last modified June 1, 2001. Version 2.
Checksum: 10AB577E04164B89
Show »

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

« Hide

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], FUNCTION, TISSUE SPECIFICITY, INDUCTION BY LIGHT.
[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. Davis R.W. Nature 408:816-820(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]	"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.
[5]	"Genetic manipulation of glycine decarboxylation." Bauwe H., Kolukisaoglu U. J. Exp. Bot. 54:1523-1535(2003) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW, NOMENCLATURE.
[6]	"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.
[7]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF228639 mRNA. Translation: AAF34795.3. AC023673 Genomic DNA. Translation: AAF79529.1. Different initiation. AC051631 Genomic DNA. Translation: AAG51522.1. CP002684 Genomic DNA. Translation: AEE32239.1. CP002684 Genomic DNA. Translation: AEE32240.1.
IPI	IPI00532806.
PIR	F96520.
RefSeq	NP_175237.1. NM_103699.4. NP_849782.1. NM_179451.1.
UniGene	At.15211.
3D structure databases
HSSP	HSSP built from PDB template 1DXL based on UniProtKB P31023.
ProteinModelPortal	Q9M5K3.
SMR	Q9M5K3. Positions 41-507.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9M5K3. 1 interaction.
Proteomic databases
PaxDb	Q9M5K3.
PRIDE	Q9M5K3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G48030.1; AT1G48030.1; AT1G48030. AT1G48030.2; AT1G48030.2; AT1G48030.
GeneID	841221.
KEGG	ath:AT1G48030.
Organism-specific databases
GeneFarm	4374. 442.
TAIR	At1g48030.
Phylogenomic databases
eggNOG	COG1249.
HOGENOM	HOG000276708.
InParanoid	Q9M5K3.
KO	K00382.
OMA	VANSRAK.
PhylomeDB	Q9M5K3.
ProtClustDB	CLSN2682168.
Gene expression databases
ArrayExpress	Q9M5K3.
Genevestigator	Q9M5K3.
GermOnline	AT1G48030. 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

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:	May 1, 2013
This is version 93 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents