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Reviewed, UniProtKB/Swiss-Prot P09624 (DLDH_YEAST)

Last modified September 23, 2008. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Dihydrolipoyl dehydrogenase, mitochondrial
    EC=1.8.1.4
Alternative name(s):
    Dihydrolipoamide dehydrogenase
    Lipoamide dehydrogenase component of pyruvate dehydrogenase complex
    Pyruvate dehydrogenase complex E3 component
    Glycine decarboxylase complex subunit L
Gene names
Name: LPD1
Synonyms: DHLP1
Ordered Locus Names: YFL018C
OrganismSaccharomyces cerevisiae (Baker's yeast) [Complete proteome]
Taxonomic identifier4932 [NCBI]
Taxonomic lineageEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length499 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 alpha-ketoacid dehydrogenase complexes. This includes the pyruvate dehydrogenase complex, which catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Acts also as component of the glycine cleavage system (glycine decarboxylase complex), which catalyzes the degradation of glycine.

Catalytic activity

Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH.

Cofactor

Binds 1 FAD per subunit By similarity.

Subunit structure

LPD1 is a homodimer. Eukaryotic pyruvate dehydrogenase (PDH) complexes are organized as a core consisting of the oligomeric dihydrolipoamide acetyl-transferase (E2), around which are arranged multiple copies of pyruvate dehydrogenase (E1), dihydrolipoamide dehydrogenase (E3) and protein X (E3BP) bound by non-covalent bonds. LPD1 is a component of the glycine decarboxylase complex (GDC), which is composed of four proteins: P, T, L and H.

Subcellular location

Mitochondrion matrix.

Miscellaneous

The active site is a redox-active disulfide bond.

Present with 24600 molecules/cell in log phase SD medium.

Sequence similarities

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

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Ontologies

Keywords

   Cellular componentMitochondrion
   DomainRedox-active center
Transit peptide
   LigandFAD
Flavoprotein
NAD
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome

Gene Ontology (GO)

   Biological process2-oxoglutarate metabolic process

Inferred from mutant phenotype. Source: SGD

L-serine biosynthetic process Ref.5

Inferred from mutant phenotype. Source: SGD

glycine catabolic process Ref.5

Inferred from mutant phenotype. Source: SGD

hydrogen peroxide metabolic process

Inferred from genetic interaction. Source: SGD

isoleucine catabolic process

Inferred from mutant phenotype. Source: SGD

leucine catabolic process

Inferred from mutant phenotype. Source: SGD

pyruvate metabolic process

Inferred from mutant phenotype. Source: SGD

valine catabolic process

Inferred from mutant phenotype. Source: SGD

   Cellular componentglycine cleavage complex Ref.5

Inferred from mutant phenotype. Source: SGD

mitochondrial nucleoid

Inferred from direct assay. Source: SGD

mitochondrial oxoglutarate dehydrogenase complex

Inferred from direct assay. Source: SGD

   Molecular functiondihydrolipoyl dehydrogenase activity

Inferred from direct assay. Source: SGD

glycine dehydrogenase (decarboxylating) activity Ref.5

Inferred from mutant phenotype. Source: SGD

oxoglutarate dehydrogenase (succinyl-transferring) activity

Inferred from mutant phenotype. Source: SGD

protein binding

Inferred from physical interaction. Source: IntAct

pyruvate dehydrogenase activity

Inferred from mutant phenotype. Source: SGD

Complete GO annotation...

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Binary interactions

With

Entry

#Exp.

IntAct

Notes

BZZ1P388221EBI-5940,EBI-3889
DML1Q036521EBI-5940,EBI-27461

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical view

Molecule processing

Transit peptide1 – 2121Mitochondrion
Chain22 – 499478Dihydrolipoyl dehydrogenase, mitochondrial

Regions

Nucleotide binding56 – 6510FAD
Nucleotide binding174 – 1763FAD By similarity
Nucleotide binding211 – 2188NAD By similarity
Nucleotide binding352 – 3554FAD

Sites

Active site4781Proton acceptor
Binding site741FAD
Binding site1391FAD; via amide nitrogen and carbonyl oxygen
Binding site2341NAD By similarity
Binding site2681NAD; via amide nitrogen and carbonyl oxygen By similarity
Binding site3051NAD; via amide nitrogen By similarity
Binding site3461FAD

Amino acid modifications

Disulfide bond65 ↔ 70Redox-active

Secondary structure

1 ............................................................................... 499
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
P09624-1 [UniParc].

Last modified July 1, 1989. Version 1.
Checksum: 986A370F2E079DBC

FASTA49954,010
        10         20         30         40         50         60 
MLRIRSLLNN KRAFSSTVRT LTINKSHDVV IIGGGPAGYV AAIKAAQLGF NTACVEKRGK 

        70         80         90        100        110        120 
LGGTCLNVGC IPSKALLNNS HLFHQMHTEA QKRGIDVNGD IKINVANFQK AKDDAVKQLT 

       130        140        150        160        170        180 
GGIELLFKKN KVTYYKGNGS FEDETKIRVT PVDGLEGTVK EDHILDVKNI IVATGSEVTP 

       190        200        210        220        230        240 
FPGIEIDEEK IVSSTGALSL KEIPKRLTII GGGIIGLEMG SVYSRLGSKV TVVEFQPQIG 

       250        260        270        280        290        300 
ASMDGEVAKA TQKFLKKQGL DFKLSTKVIS AKRNDDKNVV EIVVEDTKTN KQENLEAEVL 

       310        320        330        340        350        360 
LVAVGRRPYI AGLGAEKIGL EVDKRGRLVI DDQFNSKFPH IKVVGDVTFG PMLAHKAEEE 

       370        380        390        400        410        420 
GIAAVEMLKT GHGHVNYNNI PSVMYSHPEV AWVGKTEEQL KEAGIDYKIG KFPFAANSRA 

       430        440        450        460        470        480 
KTNQDTEGFV KILIDSKTER ILGAHIIGPN AGEMIAEAGL ALEYGASAED VARVCHAHPT 

       490 
LSEAFKEANM AAYDKAIHC

« Hide

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References

« Hide 'large scale' references
[1]"Nucleotide sequence for yeast dihydrolipoamide dehydrogenase."
Browning K.S., Uhlinger D.J., Reed L.J.
Proc. Natl. Acad. Sci. U.S.A. 85:1831-1834(1988) [PubMed: 3279419] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"The nucleotide sequence of the LPD1 gene encoding lipoamide dehydrogenase in Saccharomyces cerevisiae: comparison between eukaryotic and prokaryotic sequences for related enzymes and identification of potential upstream control sites."
Ross J., Reid G.A., Dawes I.W.
J. Gen. Microbiol. 134:1131-1139(1988) [PubMed: 3058861] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae."
Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H., Eki T.
Nat. Genet. 10:261-268(1995) [PubMed: 7670463] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
[4]Barrell B.G., Churcher C., Rajandream M.A.
Submitted (SEP-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
[5]"Genetics of the synthesis of serine from glycine and the utilization of glycine as sole nitrogen source by Saccharomyces cerevisiae."
Sinclair D.A., Dawes I.W.
Genetics 140:1213-1222(1995) [PubMed: 7498764] [Abstract]
Cited for: IDENTIFICATION IN GLYCINE DECARBOXYLASE COMPLEX.
[6]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed: 14562106] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]"Crystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast."
Toyoda T., Suzuki K., Sekiguchi T., Reed L.J., Takenaka A.
J. Biochem. 123:668-674(1998) [PubMed: 9538259] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH FAD, DISULFIDE BOND.
[8]"Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+."
Adachi W., Suzuki K., Tsunoda M., Sekiguchi T., Reed L.J., Takenaka A.
Submitted (FEB-2005) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH FAD AND NAD.
+Additional computationally mapped references.

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Cross-references

Sequence databases

J03645 mRNA. Translation: AAA34565.1.
M20880 Genomic DNA. Translation: AAB63974.1.
D50617 Genomic DNA. Translation: BAA09220.1.
Z46255 Genomic DNA. Translation: CAA86354.1.
PIRA30151.
RefSeqNP_116635.1.

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
1JEHX-ray2.40A/B22-499[»]
1V59X-ray2.20A/B22-499[»]
ModBaseSearch...

Protein-protein interaction databases

DIPDIP:41N.
IntActP09624.

Proteomic databases

PeptideAtlasP09624.

Genome annotation databases

EnsemblYFL018C. Saccharomyces cerevisiae. [Contig view]
GeneID850527.
GenomeReviewsGene locus YFL018C in contig D50617_GR.
KEGGsce:YFL018C.
NMPDRfig|4932.3.peg.2263.

Organism-specific databases

CYGDYFL018c.
SGDS000001876. LPD1.
Yeast-GFPSearch...

Phylogenomic databases

HOGENOMP09624.

Gene expression databases

ArrayExpressP09624.
GermOnlineYFL018C. Saccharomyces cerevisiae.

Family and domain databases

InterProIPR013027. FAD_pyr_nucl-diS_OxRdtase.
IPR000815. Hg_reductase.
IPR006258. Lipoamide_DHase.
IPR001100. Pyr_nuc-diS_OxRdtase.
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.
PR00411. PNDRDTASEI.
ProDomPD000139. FAD_pyr_redox. 1 hit.
[Graphical view] [Entries sharing at least one domain]