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P09624 (DLDH_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 148. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Dihydrolipoyl dehydrogenase, mitochondrial

EC=1.8.1.4
Alternative name(s):
Dihydrolipoamide dehydrogenase
Glycine decarboxylase complex subunit L
Lipoamide dehydrogenase component of pyruvate dehydrogenase complex
Pyruvate dehydrogenase complex E3 component
Gene names
Name:LPD1
Synonyms:DHLP1
Ordered Locus Names:YFL018C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length499 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

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 CO2. 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. Ref.6

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.

Ontologies

Keywords
   Cellular componentMitochondrion
   DomainRedox-active center
Transit peptide
   LigandFAD
Flavoprotein
NAD
   Molecular functionOxidoreductase
   PTMDisulfide bond
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_process2-oxoglutarate metabolic process

Inferred from mutant phenotype PubMed 3528755. Source: SGD

L-serine biosynthetic process

Inferred from mutant phenotype Ref.6. Source: SGD

cell redox homeostasis

Inferred from electronic annotation. Source: InterPro

glycine catabolic process

Inferred from mutant phenotype Ref.6. Source: SGD

hydrogen peroxide metabolic process

Inferred from mutant phenotype PubMed 17110466. Source: SGD

isoleucine catabolic process

Inferred from mutant phenotype PubMed 1479341. Source: SGD

leucine catabolic process

Inferred from mutant phenotype PubMed 1479341. Source: SGD

pyruvate metabolic process

Inferred from mutant phenotype PubMed 3528755. Source: SGD

valine catabolic process

Inferred from mutant phenotype PubMed 1479341. Source: SGD

   Cellular_componentglycine cleavage complex

Inferred from mutant phenotype Ref.6. Source: SGD

mitochondrial nucleoid

Inferred from direct assay PubMed 10869431PubMed 11926067. Source: SGD

mitochondrial oxoglutarate dehydrogenase complex

Inferred from direct assay PubMed 2072900. Source: SGD

   Molecular_functiondihydrolipoyl dehydrogenase activity

Inferred from direct assay PubMed 2821168. Source: SGD

flavin adenine dinucleotide binding

Inferred from electronic annotation. Source: InterPro

glycine dehydrogenase (decarboxylating) activity

Inferred from mutant phenotype Ref.6. Source: SGD

oxoglutarate dehydrogenase (succinyl-transferring) activity

Inferred from mutant phenotype PubMed 3528755. Source: SGD

pyruvate dehydrogenase activity

Inferred from mutant phenotype PubMed 3528755. Source: SGD

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 2121Mitochondrion Ref.1
Chain22 – 499478Dihydrolipoyl dehydrogenase, mitochondrial
PRO_0000030301

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 Ref.8

Secondary structure

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

Details...

Sequences

Sequence LengthMass (Da)Tools
P09624 [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

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]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.
[6]"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] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN GLYCINE DECARBOXYLASE COMPLEX.
[7]"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] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]"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] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH FAD, DISULFIDE BOND.
[9]"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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J03645 mRNA. Translation: AAA34565.1.
M20880 Genomic DNA. Translation: AAB63974.1.
D50617 Genomic DNA. Translation: BAA09220.1.
Z46255 Genomic DNA. Translation: CAA86354.1.
BK006940 Genomic DNA. Translation: DAA12421.1.
PIRA30151.
RefSeqNP_116635.1. NM_001179948.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JEHX-ray2.40A/B22-499[»]
1V59X-ray2.20A/B22-499[»]
ProteinModelPortalP09624.
SMRP09624. Positions 22-499.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-41N.
IntActP09624. 22 interactions.
MINTMINT-476329.
STRING4932.YFL018C.

2D gel databases

UCD-2DPAGEP09624.

Proteomic databases

PaxDbP09624.
PeptideAtlasP09624.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYFL018C; YFL018C; YFL018C.
GeneID850527.
KEGGsce:YFL018C.

Organism-specific databases

CYGDYFL018c.
SGDS000001876. LPD1.

Phylogenomic databases

eggNOGCOG1249.
GeneTreeENSGT00550000074844.
HOGENOMHOG000276708.
KOK00382.
OMAVANSRAK.
OrthoDBEOG43FM59.

Gene expression databases

GenevestigatorP09624.
GermOnlineYFL018C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D3.30.390.30. 1 hit.
InterProIPR016156. 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]
PANTHERPTHR22912:SF20. PTHR22912:SF20. 1 hit.
PfamPF00070. Pyr_redox. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
PRINTSPR00368. FADPNR.
SUPFAMSSF55424. FAD/NAD-linked_reductase_dimer. 1 hit.
TIGRFAMsTIGR01350. lipoamide_DH. 1 hit.
PROSITEPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP09624.
NextBio966268.

Entry information

Entry nameDLDH_YEAST
AccessionPrimary (citable) accession number: P09624
Secondary accession number(s): D6VTL1
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: April 3, 2013
This is version 148 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome VI

Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families