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Reviewed, UniProtKB/Swiss-Prot Q9M5K2 (DLDH2_ARATH)

Last modified June 16, 2009. Version 55. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Dihydrolipoyl dehydrogenase 2, mitochondrial
    EC=1.8.1.4
Alternative name(s):
    Dihydrolipoamide dehydrogenase 2
    Pyruvate dehydrogenase complex E3 subunit 2
      Short name=PDC-E3 2
      Short name=E3-2
    Glycine cleavage system L protein 2
Gene names
Name: LPD2
Ordered Locus Names: At3g17240
ORF Names: MGD8.7
OrganismArabidopsis thaliana (Mouse-ear cress) [Complete proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

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Protein attributes

Sequence length507 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

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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 Ref.7

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.6

Tissue specificity

Preferentially expressed in roots, flowers and siliques and at a lower level in stems and leaves. Ref.1

Miscellaneous

The active site is a redox-active disulfide bond.

Sequence similarities

Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.

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Binary interactions

With

Entry

#Exp.

IntAct

Notes

CML8O233201EBI-1237919,EBI-1237764

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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.

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 3636Mitochondrion Potential
Chain37 – 507471Dihydrolipoyl dehydrogenase 2, mitochondrial
PRO_0000260230

Regions

Nucleotide binding73 – 8210FAD By similarity
Nucleotide binding184 – 1863FAD By similarity
Nucleotide binding221 – 2288NAD By similarity
Nucleotide binding360 – 3634FAD By similarity

Sites

Active site4861Proton acceptor By similarity
Binding site911FAD By similarity
Binding site1551FAD; via amide nitrogen and carbonyl oxygen By similarity
Binding site2441NAD By similarity
Binding site2781NAD; via amide nitrogen and carbonyl oxygen By similarity
Binding site3131NAD; via amide nitrogen By similarity
Binding site3541FAD By similarity

Amino acid modifications

Disulfide bond82 ↔ 87Redox-active By similarity

Natural variations

Alternative sequence92 – 12736ALLHS…AMLAQ → VILETPFPITLIRRKFSPIF IRLLWNLLVDHHLDSI in isoform 2.
VSP_021588
Alternative sequence128 – 507380Missing in isoform 2.
VSP_021589

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Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: C5CA38074A8103D7

FASTA50753,986
        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

« Hide

Isoform 2.

Checksum: 54FBD724E3ED97E3
Show »

FASTA12713,729

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References

« Hide '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: 11598235] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY.
[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: 10819329] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[3]"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.
[4]"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).
[5]"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.
[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: 14671022] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[7]"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: 14764908] [Abstract]
Cited for: FUNCTION.

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Cross-references

Sequence databases

AF228640 mRNA. Translation: AAF34796.1.
AB022216 Genomic DNA. No translation available.
BT024578 mRNA. Translation: ABD38917.1.
AY087203 mRNA. Translation: AAM64759.1.
AJ223804 mRNA. Translation: CAA11554.1.
IPIIPI00519283.
IPI00522612.
RefSeqNP_566570.3.
NP_851005.1.
UniGeneAt.20793

3D structure databases

HSSPHSSP built from PDB template 1DXL based on UniProtKB P31023.
SMRQ9M5K2. Positions 41-507.
ModBaseSearch...

Protein-protein interaction databases

IntActQ9M5K2. 1 interaction.

Proteomic databases

PRIDEQ9M5K2.

Genome annotation databases

GeneID820984.
GenomeReviewsGene locus AT3G17240 in contig BA000014_GR.
KEGGath:AT3G17240.
NMPDRfig|3702.1.peg.13912.

Organism-specific databases

GeneFarm4375. 442.
TAIRAt3g17240.

Phylogenomic databases

OMAQ9M5K2. RILVNER.

Enzyme and pathway databases

BRENDA1.8.1.4. 302.

Gene expression databases

GermOnlineAT3G17240. Arabidopsis thaliana.

Family and domain databases

InterProIPR013027. 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]
Gene3DG3DSA:3.30.390.30. Pyr_redox_dim. 1 hit.
PANTHERPTHR22912:SF20. Lipoamide_DH. 1 hit.
PfamPF00070. Pyr_redox. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
PRINTSPR00368. FADPNR.
PR00945. HGRDTASE.
ProDomPD000139. FAD_pyr_redox. 1 hit.
[Graphical view] [Entries sharing at least one domain]
TIGRFAMsTIGR01350. lipoamide_DH. 1 hit.
PROSITEPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]
ProtoNetSearch...

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Entry information

Entry nameDLDH2_ARATH
AccessionPrimary (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: June 16, 2009
This is version 55 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectPPAP (Plant Proteome Annotation Project)

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Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents