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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)DescriptionActionsGraphical viewLength
Binding sitei74FAD2 Publications1
Binding sitei139FAD; via amide nitrogen and carbonyl oxygen2 Publications1
Binding sitei234NADBy similarity1
Binding sitei268NAD; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei305NAD; via amide nitrogenBy similarity1
Binding sitei346FAD2 Publications1
Active sitei478Proton acceptor1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi56 – 65FAD2 Publications10
Nucleotide bindingi174 – 176FADBy similarity3
Nucleotide bindingi211 – 218NADBy similarity8
Nucleotide bindingi352 – 355FAD2 Publications4

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)DescriptionActionsGraphical viewLength
Transit peptidei1 – 21Mitochondrion1 PublicationAdd BLAST21
ChainiPRO_000003030122 – 499Dihydrolipoyl dehydrogenase, mitochondrialAdd BLAST478

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi65 ↔ 70Redox-active1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

MaxQBiP09624.
PRIDEiP09624.

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 interactors.
DIPiDIP-41N.
IntActiP09624. 21 interactors.
MINTiMINT-476329.

Structurei

Secondary structure

1499
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi23 – 32Combined sources10
Helixi36 – 47Combined sources12
Beta strandi52 – 62Combined sources11
Helixi63 – 68Combined sources6
Helixi70 – 88Combined sources19
Helixi91 – 93Combined sources3
Beta strandi95 – 97Combined sources3
Beta strandi101 – 103Combined sources3
Helixi105 – 129Combined sources25
Beta strandi133 – 150Combined sources18
Beta strandi153 – 156Combined sources4
Beta strandi163 – 172Combined sources10
Beta strandi176 – 178Combined sources3
Beta strandi188 – 192Combined sources5
Helixi194 – 197Combined sources4
Beta strandi205 – 210Combined sources6
Helixi214 – 225Combined sources12
Beta strandi229 – 233Combined sources5
Beta strandi235 – 243Combined sources9
Helixi245 – 257Combined sources13
Beta strandi261 – 263Combined sources3
Beta strandi265 – 274Combined sources10
Turni275 – 278Combined sources4
Beta strandi279 – 286Combined sources8
Turni287 – 290Combined sources4
Beta strandi291 – 302Combined sources12
Beta strandi306 – 308Combined sources3
Turni311 – 313Combined sources3
Turni315 – 319Combined sources5
Beta strandi341 – 343Combined sources3
Helixi345 – 347Combined sources3
Beta strandi348 – 350Combined sources3
Helixi354 – 370Combined sources17
Helixi377 – 379Combined sources3
Beta strandi382 – 384Combined sources3
Beta strandi386 – 394Combined sources9
Helixi397 – 402Combined sources6
Beta strandi407 – 413Combined sources7
Helixi414 – 416Combined sources3
Helixi418 – 422Combined sources5
Beta strandi429 – 435Combined sources7
Turni436 – 438Combined sources3
Beta strandi440 – 448Combined sources9
Helixi451 – 463Combined sources13
Helixi468 – 472Combined sources5
Helixi483 – 493Combined sources11

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP09624.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Redox-active center, Transit peptide

Phylogenomic databases

GeneTreeiENSGT00550000074844.
HOGENOMiHOG000276708.
InParanoidiP09624.
KOiK00382.
OMAiCSDGMTK.
OrthoDBiEOG092C1XBY.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JEHX-ray2.40A/B22-499[»]
1V59X-ray2.20A/B22-499[»]
ProteinModelPortaliP09624.
SMRiP09624.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

2D gel databases

UCD-2DPAGEP09624.

Proteomic databases

MaxQBiP09624.
PRIDEiP09624.

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.
OMAiCSDGMTK.
OrthoDBiEOG092C1XBY.

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...

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: November 2, 2016
This is version 178 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.