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Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) (Glycine decarboxylase complex subunit L) (Lipoamide dehydrogenase component of pyruvate dehydrogenase complex) (Pyruvate dehydrogenase complex E3 component)

 DLDH_YEAST              Reviewed;         499 AA.
P09624; D6VTL1;
01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
01-JUL-1989, sequence version 1.
22-NOV-2017, entry version 188.
RecName: Full=Dihydrolipoyl dehydrogenase, mitochondrial;
EC=1.8.1.4;
AltName: Full=Dihydrolipoamide dehydrogenase;
AltName: Full=Glycine decarboxylase complex subunit L;
AltName: Full=Lipoamide dehydrogenase component of pyruvate dehydrogenase complex;
AltName: Full=Pyruvate dehydrogenase complex E3 component;
Flags: Precursor;
Name=LPD1; Synonyms=DHLP1; OrderedLocusNames=YFL018C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=3279419; DOI=10.1073/pnas.85.6.1831;
Browning K.S., Uhlinger D.J., Reed L.J.;
"Nucleotide sequence for yeast dihydrolipoamide dehydrogenase.";
Proc. Natl. Acad. Sci. U.S.A. 85:1831-1834(1988).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3058861; DOI=10.1099/00221287-134-5-1131;
Ross J., Reid G.A., Dawes I.W.;
"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.";
J. Gen. Microbiol. 134:1131-1139(1988).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7670463; DOI=10.1038/ng0795-261;
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.;
"Analysis of the nucleotide sequence of chromosome VI from
Saccharomyces cerevisiae.";
Nat. Genet. 10:261-268(1995).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204511 / S288c / AB972;
Barrell B.G., Churcher C., Rajandream M.A.;
Submitted (SEP-1994) to the EMBL/GenBank/DDBJ databases.
[6]
IDENTIFICATION IN GLYCINE DECARBOXYLASE COMPLEX.
PubMed=7498764;
Sinclair D.A., Dawes I.W.;
"Genetics of the synthesis of serine from glycine and the utilization
of glycine as sole nitrogen source by Saccharomyces cerevisiae.";
Genetics 140:1213-1222(1995).
[7]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[8]
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH FAD, AND
DISULFIDE BOND.
PubMed=9538259; DOI=10.1093/oxfordjournals.jbchem.a021989;
Toyoda T., Suzuki K., Sekiguchi T., Reed L.J., Takenaka A.;
"Crystal structure of eucaryotic E3, lipoamide dehydrogenase from
yeast.";
J. Biochem. 123:668-674(1998).
[9]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH FAD AND NAD.
Adachi W., Suzuki K., Tsunoda M., Sekiguchi T., Reed L.J.,
Takenaka A.;
"Crystal structure of yeast lipoamide dehydrogenase complexed with
NAD+.";
Submitted (FEB-2005) to the PDB data bank.
-!- 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 CO(2). 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:
Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
Note=Binds 1 FAD per subunit. {ECO:0000250};
-!- SUBUNIT: 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. {ECO:0000269|PubMed:7498764,
ECO:0000269|PubMed:9538259, ECO:0000269|Ref.9}.
-!- SUBCELLULAR LOCATION: Mitochondrion matrix.
-!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
-!- MISCELLANEOUS: Present with 24600 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
oxidoreductase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; J03645; AAA34565.1; -; mRNA.
EMBL; M20880; AAB63974.1; -; Genomic_DNA.
EMBL; D50617; BAA09220.1; -; Genomic_DNA.
EMBL; Z46255; CAA86354.1; -; Genomic_DNA.
EMBL; BK006940; DAA12421.1; -; Genomic_DNA.
PIR; A30151; A30151.
RefSeq; NP_116635.1; NM_001179948.1.
PDB; 1JEH; X-ray; 2.40 A; A/B=22-499.
PDB; 1V59; X-ray; 2.20 A; A/B=22-499.
PDBsum; 1JEH; -.
PDBsum; 1V59; -.
ProteinModelPortal; P09624; -.
SMR; P09624; -.
BioGrid; 31128; 428.
DIP; DIP-41N; -.
IntAct; P09624; 59.
MINT; MINT-476329; -.
STRING; 4932.YFL018C; -.
UCD-2DPAGE; P09624; -.
MaxQB; P09624; -.
PRIDE; P09624; -.
EnsemblFungi; YFL018C; YFL018C; YFL018C.
GeneID; 850527; -.
KEGG; sce:YFL018C; -.
EuPathDB; FungiDB:YFL018C; -.
SGD; S000001876; LPD1.
GeneTree; ENSGT00550000074844; -.
HOGENOM; HOG000276708; -.
InParanoid; P09624; -.
KO; K00382; -.
OMA; TMSEAVM; -.
OrthoDB; EOG092C1XBY; -.
BioCyc; YEAST:YFL018C-MONOMER; -.
Reactome; R-SCE-204174; Regulation of pyruvate dehydrogenase (PDH) complex.
Reactome; R-SCE-389661; Glyoxylate metabolism and glycine degradation.
Reactome; R-SCE-5362517; Signaling by Retinoic Acid.
Reactome; R-SCE-6783984; Glycine degradation.
Reactome; R-SCE-70268; Pyruvate metabolism.
Reactome; R-SCE-70895; Branched-chain amino acid catabolism.
Reactome; R-SCE-71064; Lysine catabolism.
Reactome; R-SCE-71403; Citric acid cycle (TCA cycle).
EvolutionaryTrace; P09624; -.
PRO; PR:P09624; -.
Proteomes; UP000002311; Chromosome VI.
GO; GO:0005960; C:glycine cleavage complex; IMP:SGD.
GO; GO:0042645; C:mitochondrial nucleoid; IDA:SGD.
GO; GO:0009353; C:mitochondrial oxoglutarate dehydrogenase complex; IDA:SGD.
GO; GO:0005967; C:mitochondrial pyruvate dehydrogenase complex; IDA:SGD.
GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IDA:SGD.
GO; GO:0009055; F:electron carrier activity; IEA:InterPro.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
GO; GO:0004375; F:glycine dehydrogenase (decarboxylating) activity; IMP:SGD.
GO; GO:0004591; F:oxoglutarate dehydrogenase (succinyl-transferring) activity; IMP:SGD.
GO; GO:0004738; F:pyruvate dehydrogenase activity; IMP:SGD.
GO; GO:0006103; P:2-oxoglutarate metabolic process; IMP:SGD.
GO; GO:0045454; P:cell redox homeostasis; IEA:InterPro.
GO; GO:0006546; P:glycine catabolic process; IMP:SGD.
GO; GO:0042743; P:hydrogen peroxide metabolic process; IMP:SGD.
GO; GO:0006550; P:isoleucine catabolic process; IMP:SGD.
GO; GO:0006564; P:L-serine biosynthetic process; IMP:SGD.
GO; GO:0006552; P:leucine catabolic process; IMP:SGD.
GO; GO:0006090; P:pyruvate metabolic process; IMP:SGD.
GO; GO:0006574; P:valine catabolic process; IMP:SGD.
Gene3D; 3.30.390.30; -; 1.
Gene3D; 3.50.50.60; -; 1.
InterPro; IPR036188; FAD/NAD-bd_sf.
InterPro; IPR023753; FAD/NAD-binding_dom.
InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer_sf.
InterPro; IPR006258; Lipoamide_DH.
InterPro; IPR001100; Pyr_nuc-diS_OxRdtase.
InterPro; IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
InterPro; IPR012999; Pyr_OxRdtase_I_AS.
Pfam; PF07992; Pyr_redox_2; 1.
Pfam; PF02852; Pyr_redox_dim; 1.
PIRSF; PIRSF000350; Mercury_reductase_MerA; 1.
SUPFAM; SSF51905; SSF51905; 1.
SUPFAM; SSF55424; SSF55424; 1.
TIGRFAMs; TIGR01350; lipoamide_DH; 1.
PROSITE; PS00076; PYRIDINE_REDOX_1; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Disulfide bond; FAD; Flavoprotein;
Mitochondrion; NAD; Oxidoreductase; Redox-active center;
Reference proteome; Transit peptide.
TRANSIT 1 21 Mitochondrion.
{ECO:0000269|PubMed:3279419}.
CHAIN 22 499 Dihydrolipoyl dehydrogenase,
mitochondrial.
/FTId=PRO_0000030301.
NP_BIND 56 65 FAD. {ECO:0000269|PubMed:9538259,
ECO:0000269|Ref.9}.
NP_BIND 174 176 FAD. {ECO:0000250}.
NP_BIND 211 218 NAD. {ECO:0000250}.
NP_BIND 352 355 FAD. {ECO:0000269|PubMed:9538259,
ECO:0000269|Ref.9}.
ACT_SITE 478 478 Proton acceptor.
BINDING 74 74 FAD. {ECO:0000269|PubMed:9538259,
ECO:0000269|Ref.9}.
BINDING 139 139 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000269|PubMed:9538259,
ECO:0000269|Ref.9}.
BINDING 234 234 NAD. {ECO:0000250}.
BINDING 268 268 NAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000250}.
BINDING 305 305 NAD; via amide nitrogen. {ECO:0000250}.
BINDING 346 346 FAD. {ECO:0000269|PubMed:9538259,
ECO:0000269|Ref.9}.
DISULFID 65 70 Redox-active.
{ECO:0000269|PubMed:9538259}.
STRAND 23 32 {ECO:0000244|PDB:1V59}.
HELIX 36 47 {ECO:0000244|PDB:1V59}.
STRAND 52 62 {ECO:0000244|PDB:1V59}.
HELIX 63 68 {ECO:0000244|PDB:1V59}.
HELIX 70 88 {ECO:0000244|PDB:1V59}.
HELIX 91 93 {ECO:0000244|PDB:1V59}.
STRAND 95 97 {ECO:0000244|PDB:1V59}.
STRAND 101 103 {ECO:0000244|PDB:1V59}.
HELIX 105 129 {ECO:0000244|PDB:1V59}.
STRAND 133 150 {ECO:0000244|PDB:1V59}.
STRAND 153 156 {ECO:0000244|PDB:1JEH}.
STRAND 163 172 {ECO:0000244|PDB:1V59}.
STRAND 176 178 {ECO:0000244|PDB:1V59}.
STRAND 188 192 {ECO:0000244|PDB:1V59}.
HELIX 194 197 {ECO:0000244|PDB:1V59}.
STRAND 205 210 {ECO:0000244|PDB:1V59}.
HELIX 214 225 {ECO:0000244|PDB:1V59}.
STRAND 229 233 {ECO:0000244|PDB:1V59}.
STRAND 235 243 {ECO:0000244|PDB:1V59}.
HELIX 245 257 {ECO:0000244|PDB:1V59}.
STRAND 261 263 {ECO:0000244|PDB:1V59}.
STRAND 265 274 {ECO:0000244|PDB:1V59}.
TURN 275 278 {ECO:0000244|PDB:1V59}.
STRAND 279 286 {ECO:0000244|PDB:1V59}.
TURN 287 290 {ECO:0000244|PDB:1V59}.
STRAND 291 302 {ECO:0000244|PDB:1V59}.
STRAND 306 308 {ECO:0000244|PDB:1V59}.
TURN 311 313 {ECO:0000244|PDB:1JEH}.
TURN 315 319 {ECO:0000244|PDB:1V59}.
STRAND 341 343 {ECO:0000244|PDB:1V59}.
HELIX 345 347 {ECO:0000244|PDB:1V59}.
STRAND 348 350 {ECO:0000244|PDB:1V59}.
HELIX 354 370 {ECO:0000244|PDB:1V59}.
HELIX 377 379 {ECO:0000244|PDB:1JEH}.
STRAND 382 384 {ECO:0000244|PDB:1V59}.
STRAND 386 394 {ECO:0000244|PDB:1V59}.
HELIX 397 402 {ECO:0000244|PDB:1V59}.
STRAND 407 413 {ECO:0000244|PDB:1V59}.
HELIX 414 416 {ECO:0000244|PDB:1V59}.
HELIX 418 422 {ECO:0000244|PDB:1V59}.
STRAND 429 435 {ECO:0000244|PDB:1V59}.
TURN 436 438 {ECO:0000244|PDB:1V59}.
STRAND 440 448 {ECO:0000244|PDB:1V59}.
HELIX 451 463 {ECO:0000244|PDB:1V59}.
HELIX 468 472 {ECO:0000244|PDB:1V59}.
HELIX 483 493 {ECO:0000244|PDB:1V59}.
SEQUENCE 499 AA; 54010 MW; 986A370F2E079DBC CRC64;
MLRIRSLLNN KRAFSSTVRT LTINKSHDVV IIGGGPAGYV AAIKAAQLGF NTACVEKRGK
LGGTCLNVGC IPSKALLNNS HLFHQMHTEA QKRGIDVNGD IKINVANFQK AKDDAVKQLT
GGIELLFKKN KVTYYKGNGS FEDETKIRVT PVDGLEGTVK EDHILDVKNI IVATGSEVTP
FPGIEIDEEK IVSSTGALSL KEIPKRLTII GGGIIGLEMG SVYSRLGSKV TVVEFQPQIG
ASMDGEVAKA TQKFLKKQGL DFKLSTKVIS AKRNDDKNVV EIVVEDTKTN KQENLEAEVL
LVAVGRRPYI AGLGAEKIGL EVDKRGRLVI DDQFNSKFPH IKVVGDVTFG PMLAHKAEEE
GIAAVEMLKT GHGHVNYNNI PSVMYSHPEV AWVGKTEEQL KEAGIDYKIG KFPFAANSRA
KTNQDTEGFV KILIDSKTER ILGAHIIGPN AGEMIAEAGL ALEYGASAED VARVCHAHPT
LSEAFKEANM AAYDKAIHC


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