Dihydrolipoyl dehydrogenase, mitochondrial precursor - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P09624 (DLDH_YEAST)

Last modified June 16, 2009. Version 110. History...

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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 names

Recommended 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

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

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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.

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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 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.
Subcellular location	Mitochondrion matrix.
Miscellaneous	The active site is a redox-active disulfide bond. Present with 24600 molecules/cell in log phase SD medium. Ref.6
Sequence similarities	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.

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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
Gene Ontology (GO)
Biological process	2-oxoglutarate metabolic process Inferred from mutant phenotype. Source: SGD L-serine biosynthetic process Ref.5 Inferred from mutant phenotype. Source: SGD cell redox homeostasis Inferred from electronic annotation. Source: InterPro 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 oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW pyruvate metabolic process Inferred from mutant phenotype. Source: SGD valine catabolic process Inferred from mutant phenotype. Source: SGD
Cellular component	glycine 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 function	FAD binding Inferred from electronic annotation. Source: InterPro dihydrolipoyl 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
BZZ1	P38822	1	EBI-5940,EBI-3889
DML1	Q03652	1	EBI-5940,EBI-27461

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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.7

Secondary structure

499

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P09624-1 [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

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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: 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.

PIR

A30151.

RefSeq

NP_116635.1.

3D structure databases

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:41N.

IntAct

P09624. 34 interactions.

Proteomic databases

PeptideAtlas

P09624.

PRIDE

P09624.

Genome annotation databases

Ensembl

YFL018C. Saccharomyces cerevisiae. [Contig view]

GeneID

850527.

GenomeReviews

Gene locus YFL018C in contig D50617_GR.

KEGG

sce:YFL018C.

NMPDR

fig|4932.3.peg.2263.

Organism-specific databases

CYGD

YFL018c.

SGD

S000001876. LPD1.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P09624.

OMA

P09624. ECINRAC.

Enzyme and pathway databases

BRENDA

1.8.1.4. 250.

Gene expression databases

ArrayExpress

P09624.

GermOnline

YFL018C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR013027. FAD_pyr_nucl-diS_OxRdtase.
IPR000815. Hg_reductase.
IPR006258. Lipoamide_DH.
IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
IPR012999. Pyr_OxRdtase_I_AS.
IPR001327. Pyr_OxRdtase_NAD_bd.
[Graphical view]

Gene3D

G3DSA:3.30.390.30. Pyr_redox_dim. 1 hit.

PANTHER

PTHR22912:SF20. Lipoamide_DH. 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.
PR00945. HGRDTASE.

ProDom

PD000139. FAD_pyr_redox. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR01350. lipoamide_DH. 1 hit.

PROSITE

PS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

966268.

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Entry information

Entry name

DLDH_YEAST

Accession

Primary (citable) accession number: P09624

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	July 1, 1989
Last modified:	June 16, 2009
This is version 110 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

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

Yeast chromosome VI

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

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

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

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents