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Protein

Dihydrolipoyl dehydrogenase, mitochondrial

Gene

LPD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

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

Cofactori

FADBy similarityNote: Binds 1 FAD per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei74 – 741FAD2 Publications
Binding sitei139 – 1391FAD; via amide nitrogen and carbonyl oxygen2 Publications
Binding sitei234 – 2341NADBy similarity
Binding sitei268 – 2681NAD; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei305 – 3051NAD; via amide nitrogenBy similarity
Binding sitei346 – 3461FAD2 Publications
Active sitei478 – 4781Proton acceptor

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi56 – 6510FAD2 Publications
Nucleotide bindingi174 – 1763FADBy similarity
Nucleotide bindingi211 – 2188NADBy similarity
Nucleotide bindingi352 – 3554FAD2 Publications

GO - Molecular functioni

  • dihydrolipoyl dehydrogenase activity Source: SGD
  • flavin adenine dinucleotide binding Source: InterPro
  • glycine dehydrogenase (decarboxylating) activity Source: SGD
  • oxoglutarate dehydrogenase (succinyl-transferring) activity Source: SGD
  • pyruvate dehydrogenase activity Source: SGD

GO - Biological processi

  • 2-oxoglutarate metabolic process Source: SGD
  • cell redox homeostasis Source: InterPro
  • glycine catabolic process Source: SGD
  • hydrogen peroxide metabolic process Source: SGD
  • isoleucine catabolic process Source: SGD
  • leucine catabolic process Source: SGD
  • L-serine biosynthetic process Source: SGD
  • pyruvate metabolic process Source: SGD
  • valine catabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

FAD, Flavoprotein, NAD

Enzyme and pathway databases

BioCyciYEAST:YFL018C-MONOMER.
ReactomeiR-SCE-204174. Regulation of pyruvate dehydrogenase (PDH) complex.
R-SCE-389661. Glyoxylate metabolism and glycine degradation.
R-SCE-5362517. Signaling by Retinoic Acid.
R-SCE-6783984. Glycine degradation.
R-SCE-70268. Pyruvate metabolism.
R-SCE-70895. Branched-chain amino acid catabolism.
R-SCE-71064. Lysine catabolism.
R-SCE-71403. Citric acid cycle (TCA cycle).

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:LPD1
Synonyms:DHLP1
Ordered Locus Names:YFL018C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VI

Organism-specific databases

EuPathDBiFungiDB:YFL018C.
SGDiS000001876. LPD1.

Subcellular locationi

GO - Cellular componenti

  • glycine cleavage complex Source: SGD
  • mitochondrial nucleoid Source: SGD
  • mitochondrial oxoglutarate dehydrogenase complex Source: SGD
  • mitochondrial pyruvate dehydrogenase complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 2121Mitochondrion1 PublicationAdd
BLAST
Chaini22 – 499478Dihydrolipoyl dehydrogenase, mitochondrialPRO_0000030301Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi65 ↔ 70Redox-active1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

MaxQBiP09624.

2D gel databases

UCD-2DPAGEP09624.

Interactioni

Subunit structurei

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.3 Publications

Protein-protein interaction databases

BioGridi31128. 55 interactions.
DIPiDIP-41N.
IntActiP09624. 21 interactions.
MINTiMINT-476329.

Structurei

Secondary structure

1
499
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi23 – 3210Combined sources
Helixi36 – 4712Combined sources
Beta strandi52 – 6211Combined sources
Helixi63 – 686Combined sources
Helixi70 – 8819Combined sources
Helixi91 – 933Combined sources
Beta strandi95 – 973Combined sources
Beta strandi101 – 1033Combined sources
Helixi105 – 12925Combined sources
Beta strandi133 – 15018Combined sources
Beta strandi153 – 1564Combined sources
Beta strandi163 – 17210Combined sources
Beta strandi176 – 1783Combined sources
Beta strandi188 – 1925Combined sources
Helixi194 – 1974Combined sources
Beta strandi205 – 2106Combined sources
Helixi214 – 22512Combined sources
Beta strandi229 – 2335Combined sources
Beta strandi235 – 2439Combined sources
Helixi245 – 25713Combined sources
Beta strandi261 – 2633Combined sources
Beta strandi265 – 27410Combined sources
Turni275 – 2784Combined sources
Beta strandi279 – 2868Combined sources
Turni287 – 2904Combined sources
Beta strandi291 – 30212Combined sources
Beta strandi306 – 3083Combined sources
Turni311 – 3133Combined sources
Turni315 – 3195Combined sources
Beta strandi341 – 3433Combined sources
Helixi345 – 3473Combined sources
Beta strandi348 – 3503Combined sources
Helixi354 – 37017Combined sources
Helixi377 – 3793Combined sources
Beta strandi382 – 3843Combined sources
Beta strandi386 – 3949Combined sources
Helixi397 – 4026Combined sources
Beta strandi407 – 4137Combined sources
Helixi414 – 4163Combined sources
Helixi418 – 4225Combined sources
Beta strandi429 – 4357Combined sources
Turni436 – 4383Combined sources
Beta strandi440 – 4489Combined sources
Helixi451 – 46313Combined sources
Helixi468 – 4725Combined sources
Helixi483 – 49311Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JEHX-ray2.40A/B22-499[»]
1V59X-ray2.20A/B22-499[»]
ProteinModelPortaliP09624.
SMRiP09624. Positions 22-499.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09624.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Redox-active center, Transit peptide

Phylogenomic databases

GeneTreeiENSGT00550000074844.
HOGENOMiHOG000276708.
InParanoidiP09624.
KOiK00382.
OMAiVYTQPEI.
OrthoDBiEOG7K0ZNC.

Family and domain databases

Gene3Di3.30.390.30. 1 hit.
3.50.50.60. 2 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR016156. FAD/NAD-linked_Rdtase_dimer.
IPR006258. Lipoamide_DH.
IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
IPR012999. Pyr_OxRdtase_I_AS.
[Graphical view]
PfamiPF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
SSF55424. SSF55424. 1 hit.
TIGRFAMsiTIGR01350. lipoamide_DH. 1 hit.
PROSITEiPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P09624-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRIRSLLNN KRAFSSTVRT LTINKSHDVV IIGGGPAGYV AAIKAAQLGF
60 70 80 90 100
NTACVEKRGK LGGTCLNVGC IPSKALLNNS HLFHQMHTEA QKRGIDVNGD
110 120 130 140 150
IKINVANFQK AKDDAVKQLT GGIELLFKKN KVTYYKGNGS FEDETKIRVT
160 170 180 190 200
PVDGLEGTVK EDHILDVKNI IVATGSEVTP FPGIEIDEEK IVSSTGALSL
210 220 230 240 250
KEIPKRLTII GGGIIGLEMG SVYSRLGSKV TVVEFQPQIG ASMDGEVAKA
260 270 280 290 300
TQKFLKKQGL DFKLSTKVIS AKRNDDKNVV EIVVEDTKTN KQENLEAEVL
310 320 330 340 350
LVAVGRRPYI AGLGAEKIGL EVDKRGRLVI DDQFNSKFPH IKVVGDVTFG
360 370 380 390 400
PMLAHKAEEE GIAAVEMLKT GHGHVNYNNI PSVMYSHPEV AWVGKTEEQL
410 420 430 440 450
KEAGIDYKIG KFPFAANSRA KTNQDTEGFV KILIDSKTER ILGAHIIGPN
460 470 480 490
AGEMIAEAGL ALEYGASAED VARVCHAHPT LSEAFKEANM AAYDKAIHC
Length:499
Mass (Da):54,010
Last modified:July 1, 1989 - v1
Checksum:i986A370F2E079DBC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA30151.
RefSeqiNP_116635.1. NM_001179948.1.

Genome annotation databases

EnsemblFungiiBAA09220; BAA09220; BAA09220.
YFL018C; YFL018C; YFL018C.
GeneIDi850527.
KEGGisce:YFL018C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA30151.
RefSeqiNP_116635.1. NM_001179948.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JEHX-ray2.40A/B22-499[»]
1V59X-ray2.20A/B22-499[»]
ProteinModelPortaliP09624.
SMRiP09624. Positions 22-499.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31128. 55 interactions.
DIPiDIP-41N.
IntActiP09624. 21 interactions.
MINTiMINT-476329.

2D gel databases

UCD-2DPAGEP09624.

Proteomic databases

MaxQBiP09624.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiBAA09220; BAA09220; BAA09220.
YFL018C; YFL018C; YFL018C.
GeneIDi850527.
KEGGisce:YFL018C.

Organism-specific databases

EuPathDBiFungiDB:YFL018C.
SGDiS000001876. LPD1.

Phylogenomic databases

GeneTreeiENSGT00550000074844.
HOGENOMiHOG000276708.
InParanoidiP09624.
KOiK00382.
OMAiVYTQPEI.
OrthoDBiEOG7K0ZNC.

Enzyme and pathway databases

BioCyciYEAST:YFL018C-MONOMER.
ReactomeiR-SCE-204174. Regulation of pyruvate dehydrogenase (PDH) complex.
R-SCE-389661. Glyoxylate metabolism and glycine degradation.
R-SCE-5362517. Signaling by Retinoic Acid.
R-SCE-6783984. Glycine degradation.
R-SCE-70268. Pyruvate metabolism.
R-SCE-70895. Branched-chain amino acid catabolism.
R-SCE-71064. Lysine catabolism.
R-SCE-71403. Citric acid cycle (TCA cycle).

Miscellaneous databases

EvolutionaryTraceiP09624.
PROiP09624.

Family and domain databases

Gene3Di3.30.390.30. 1 hit.
3.50.50.60. 2 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR016156. FAD/NAD-linked_Rdtase_dimer.
IPR006258. Lipoamide_DH.
IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
IPR012999. Pyr_OxRdtase_I_AS.
[Graphical view]
PfamiPF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
SSF55424. SSF55424. 1 hit.
TIGRFAMsiTIGR01350. lipoamide_DH. 1 hit.
PROSITEiPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. 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. 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.

Entry informationi

Entry nameiDLDH_YEAST
AccessioniPrimary (citable) accession number: P09624
Secondary accession number(s): D6VTL1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: July 6, 2016
This is version 175 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

The active site is a redox-active disulfide bond.
Present with 24600 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VI
    Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.