Dihydrolipoyl dehydrogenase, mitochondrial precursor - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P09624 (DLDH_YEAST) Reviewed, UniProtKB/Swiss-Prot

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

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	LPD1
Synonyms:	DHLP1
Ordered Locus Names:	YFL018C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	499 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 component	Mitochondrion
Domain	Redox-active center Transit peptide
Ligand	FAD Flavoprotein NAD
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	2-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_component	glycine cleavage complex Inferred from mutant phenotype Ref.6. Source: SGD mitochondrial nucleoid Inferred from direct assay PubMed 10869431 PubMed 11926067. Source: SGD mitochondrial oxoglutarate dehydrogenase complex Inferred from direct assay PubMed 2072900. Source: SGD
Molecular_function	dihydrolipoyl 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 21

Mitochondrion Ref.1

Chain

22 – 499

478

Dihydrolipoyl dehydrogenase, mitochondrial

PRO_0000030301

Regions

Nucleotide binding

56 – 65

FAD

Nucleotide binding

174 – 176

FAD By similarity

Nucleotide binding

211 – 218

NAD By similarity

Nucleotide binding

352 – 355

FAD

Sites

Active site

478

Proton acceptor

Binding site

FAD

Binding site

139

FAD; via amide nitrogen and carbonyl oxygen

Binding site

234

NAD By similarity

Binding site

268

NAD; via amide nitrogen and carbonyl oxygen By similarity

Binding site

305

NAD; via amide nitrogen By similarity

Binding site

346

FAD

Amino acid modifications

Disulfide bond

65 ↔ 70

Redox-active Ref.8

Secondary structure

499

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P09624 [UniParc].

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

FASTA

499

54,010

        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' referencesShow '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.

PIR

A30151.

RefSeq

NP_116635.1. NM_001179948.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JEH	X-ray	2.40	A/B	22-499	[»]
1V59	X-ray	2.20	A/B	22-499	[»]

ProteinModelPortal

P09624.

SMR

P09624. Positions 22-499.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-41N.

IntAct

P09624. 22 interactions.

MINT

MINT-476329.

STRING

4932.YFL018C.

2D gel databases

UCD-2DPAGE

P09624.

Proteomic databases

PaxDb

P09624.

PeptideAtlas

P09624.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YFL018C; YFL018C; YFL018C.

GeneID

850527.

KEGG

sce:YFL018C.

Organism-specific databases

CYGD

YFL018c.

SGD

S000001876. LPD1.

Phylogenomic databases

eggNOG

COG1249.

GeneTree

ENSGT00550000074844.

HOGENOM

HOG000276708.

K00382.

OMA

VANSRAK.

OrthoDB

EOG43FM59.

Gene expression databases

Genevestigator

P09624.

GermOnline

YFL018C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.30.390.30. 1 hit.

InterPro

IPR016156. 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]

PANTHER

PTHR22912:SF20. PTHR22912:SF20. 1 hit.

Pfam

PF00070. Pyr_redox. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]

PRINTS

PR00368. FADPNR.

SUPFAM

SSF55424. FAD/NAD-linked_reductase_dimer. 1 hit.

TIGRFAMs

TIGR01350. lipoamide_DH. 1 hit.

PROSITE

PS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P09624.

NextBio

966268.

Entry information

Entry name

DLDH_YEAST

Accession

Primary (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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal 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

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents