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UniProtKB/Swiss-Prot entry P09622


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name DLDH_HUMAN
Primary accession number P09622
Secondary accession numbers Q14131 Q14167 Q59EV8 Q8WTS4
Integrated into Swiss-Prot on July 1, 1989
Sequence was last modified on July 1, 1989 (Sequence version 1)
Annotations were last modified on    December 16, 2008 (Entry version 119)
Name and origin of the protein
Protein name Dihydrolipoyl dehydrogenase, mitochondrial [Precursor]
Synonyms EC 1.8.1.4
Dihydrolipoamide dehydrogenase
Glycine cleavage system L protein
Gene name
Name: DLD
Synonyms: GCSL, LAD, PHE3
From
Homo sapiens (Human) [TaxID: 9606] 
Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=3693355 [NCBI, ExPASy, EBI, Israel, Japan]
Otulakowski G., Robinson B.H.;
"Isolation and sequence determination of cDNA clones for porcine and human lipoamide dehydrogenase. Homology to other disulfide oxidoreductases.";
J. Biol. Chem. 262:17313-17318(1987).
[2]
NUCLEOTIDE SEQUENCE [MRNA], AND VARIANT LYS-104.
PubMed=3278312 [NCBI, ExPASy, EBI, Israel, Japan]
Pons G., Raefsky-Estrin C., Carothers D.J., Pepin R.A., Javed A.A., Jesse B.W., Ganapathi M.K., Samols D., Patel M.S.;
"Cloning and cDNA sequence of the dihydrolipoamide dehydrogenase component human alpha-ketoacid dehydrogenase complexes.";
Proc. Natl. Acad. Sci. U.S.A. 85:1422-1426(1988).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
TISSUE=Liver;
DOI=10.1006/geno.1993.1335; PubMed=8406489 [NCBI, ExPASy, EBI, Israel, Japan]
Feigenbaum A.S., Robinson B.H.;
"The structure of the human dihydrolipoamide dehydrogenase gene (DLD) and its upstream elements.";
Genomics 17:376-381(1993).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT LYS-104.
TISSUE=Brain;
Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S., Ohara O., Nagase T., Kikuno R.F.;
Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
DOI=10.1126/science.1083423; PubMed=12690205 [NCBI, ExPASy, EBI, Israel, Japan]
Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S., Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.;
"Human chromosome 7: DNA sequence and biology.";
Science 300:767-772(2003).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT LYS-104.
TISSUE=Ovary;
DOI=10.1101/gr.2596504; PubMed=15489334 [NCBI, ExPASy, EBI, Israel, Japan]
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-13.
PubMed=1332063 [NCBI, ExPASy, EBI, Israel, Japan]
Johanning G.L., Morris J.I., Madhusudhan K.T., Samols D., Patel M.S.;
"Characterization of the transcriptional regulatory region of the human dihydrolipoamide dehydrogenase gene.";
Proc. Natl. Acad. Sci. U.S.A. 89:10964-10968(1992).
[8]
X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF 36-509 IN COMPLEXES WITH NAD AND FAD, AND SUBUNIT.
DOI=10.1016/j.jmb.2005.05.014; PubMed=15946682 [NCBI, ExPASy, EBI, Israel, Japan]
Brautigam C.A., Chuang J.L., Tomchick D.R., Machius M., Chuang D.T.;
"Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations.";
J. Mol. Biol. 350:543-552(2005).
[9]
X-RAY CRYSTALLOGRAPHY (2.59 ANGSTROMS) OF 36-509.
DOI=10.1074/jbc.M507850200; PubMed=16263718 [NCBI, ExPASy, EBI, Israel, Japan]
Ciszak E.M., Makal A., Hong Y.S., Vettaikkorumakankauv A.K., Korotchkina L.G., Patel M.S.;
"How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex.";
J. Biol. Chem. 281:648-655(2006).
[10]
X-RAY CRYSTALLOGRAPHY (2.18 ANGSTROMS) OF 36-509 IN COMPLEX WITH PDHX, AND CHARACTERIZATION OF VARIANT DLD DEFICIENCY GLY-495.
DOI=10.1016/j.str.2006.01.001; PubMed=16442803 [NCBI, ExPASy, EBI, Israel, Japan]
Brautigam C.A., Wynn R.M., Chuang J.L., Machius M., Tomchick D.R., Chuang D.T.;
"Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex.";
Structure 14:611-621(2006).
[11]
VARIANTS DLD DEFICIENCY GLU-72 AND LEU-488.
PubMed=8506365 [NCBI, ExPASy, EBI, Israel, Japan]
Liu T.-C., Kim H., Arizmendi C., Kitano A., Patel M.S.;
"Identification of two missense mutations in a dihydrolipoamide dehydrogenase-deficient patient.";
Proc. Natl. Acad. Sci. U.S.A. 90:5186-5190(1993).
[12]
VARIANT DLD DEFICIENCY GLY-495.
DOI=10.1093/hmg/5.12.1925; PubMed=8968745 [NCBI, ExPASy, EBI, Israel, Japan]
Hong Y.S., Kerr D.S., Craigen W.J., Tan J., Pan Y., Lusk M., Patel M.S.;
"Identification of two mutations in a compound heterozygous child with dihydrolipoamide dehydrogenase deficiency.";
Hum. Mol. Genet. 5:1925-1930(1996).
[13]
VARIANT DLD DEFICIENCY CYS-229.
DOI=10.1002/(SICI)1096-8628(19990115)82:2<177::AID-AJMG15>3.3.CO;2-0; PubMed=9934985 [NCBI, ExPASy, EBI, Israel, Japan]
Shaag A., Saada A., Berger I., Mandel H., Joseph A., Feigenbaum A., Elpeleg O.N.;
"Molecular basis of lipoamide dehydrogenase deficiency in Ashkenazi Jews.";
Am. J. Med. Genet. 82:177-182(1999).
Comments
  • FUNCTION: Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes.
  • CATALYTIC ACTIVITY: Protein N6-(dihydrolipoyl)lysine + NAD+ = protein N6-(lipoyl)lysine + NADH.
  • COFACTOR: Binds 1 FAD per subunit (By similarity).
  • SUBUNIT: Homodimer. Eukaryotic pyruvate dehydrogenase complexes are organized about a core consisting of the oligomeric dihydrolipoamide acetyl-transferase, around which are arranged multiple copies of pyruvate dehydrogenase, dihydrolipoamide dehydrogenase and protein X bound by non-covalent bonds.
  • SUBCELLULAR LOCATION: Mitochondrion matrix.
  • DISEASE: Defects in DLD are a cause of congenital infantile lactic acidosis.
  • DISEASE: Defects in DLD are a cause of maple syrup urine disease (MSUD) [MIM:248600]. MSUD is characterized by mental and physical retardation, feeding problems and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine, resulting from a block in oxidative decarboxylation.
  • MISCELLANEOUS: The active site is a redox-active disulfide bond.
  • SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.
  • WEB RESOURCE: Name=GeneReviews; URL="http://www.genetests.org/query?gene=DLD";.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
J03490; AAA59527.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
J03620; AAA35764.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13761; AAB01381.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13749; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13750; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13751; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13752; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13753; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13754; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13748; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13755; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13759; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13760; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13756; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13757; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
L13758; AAB01381.1; JOINED; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AB209703; BAD92940.1; ALT_INIT; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
CH236947; EAL24389.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC018648; AAH18648.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC018696; AAH18696.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
M99384; AAA35759.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR A92622; DEHULP.
UniGene Hs.131711
3D structure databases
PDB
1ZMC; X-ray; 2.53 A; A/B/C/D/E/F/G/H=36-509.[ExPASy / RCSB / EBI]
1ZMD; X-ray; 2.08 A; A/B/C/D/E/F/G/H=36-509.[ExPASy / RCSB / EBI]
1ZY8; X-ray; 2.59 A; A/B/C/D/E/F/G/H/I/J=36-509.[ExPASy / RCSB / EBI]
2F5Z; X-ray; 2.18 A; A/B/C/D/E/F/G/H/I/J=36-509.[ExPASy / RCSB / EBI]
Detailed list of linked structures.
PDBsum 1ZMC; -.
1ZMD; -.
1ZY8; -.
2F5Z; -.
ModBase P09622.
Protein-protein interaction databases
DIP DIP:29027N; -.
PTM databases
PhosphoSite P09622; -.
Enzyme and pathway databases
BioCyc MetaCyc:MON-12008; -.
Reactome REACT_1046; Pyruvate metabolism and TCA cycle.
REACT_13; Metabolism of amino acids.
2D gel databases
HSC-2DPAGE P09622; -.
REPRODUCTION-2DPAGE IPI00015911; -.
Organism-specific databases
GeneCards GC07P107318; -.
H-InvDB HIX0006994; -.
HGNC HGNC:2898; DLD.
GenAtlas DLD.
MIM 238331; gene. [NCBI / EBI]
248600; phenotype. [NCBI / EBI]
Orphanet 506; Leigh syndrome.
511; Leucinosis.
2394; Lipoamide dehydrogenase deficiency.
765; Pyruvate dehydrogenase deficiency.
PharmGKB PA27352; -.
GeneCards P09622.
Gene expression databases
ArrayExpress P09622; -.
CleanEx HS_DLD; -.
GermOnline ENSG00000091140; Homo sapiens.
Ontologies
GO
GO:0005759; Cellular component: mitochondrial matrix (inferred from electronic annotation from UniProtKB-SubCell).
GO:0004148; Molecular function: dihydrolipoyl dehydrogenase activity (traceable author statement from ProtInc).
GO:0050660; Molecular function: FAD binding (inferred from electronic annotation from InterPro).
GO:0045454; Biological process: cell redox homeostasis (inferred from electronic annotation from InterPro).
GO:0055114; Biological process: oxidation reduction (inferred from electronic annotation from UniProtKB-KW).
QuickGo view.
Family and domain databases
InterPro IPR013027; FAD_pyr_nucl-diS_OxRdtase.
IPR000815; Hg_reductase.
IPR006258; Lipoamide_DHase.
IPR001100; Pyr_nuc-diS_OxRdtase.
IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
IPR012999; Pyr_OxRdtase_I_AS.
IPR001327; Pyr_OxRdtase_NAD_bd.
Graphical view of domain structure.
Gene3D G3DSA:3.30.390.30; Pyr_redox_dim; 1.
PANTHER PTHR22912:SF20; Lipoamide_DH; 1.
Pfam PF00070; Pyr_redox; 1.
PF07992; Pyr_redox_2; 1.
PF02852; Pyr_redox_dim; 1.
Pfam graphical view of domain structure.
PRINTS PR00368; FADPNR.
PR00945; HGRDTASE.
PR00411; PNDRDTASEI.
ProDom PD000139; FAD_pyr_redox; 1.
[Domain structure / List of seq. sharing at least 1 domain]
TIGRFAMs TIGR01350; lipoamide_DH; 1.
PROSITE PS00076; PYRIDINE_REDOX_1; 1.
Proteomics databases
PRIDE P09622; -.
Genome annotation databases
Ensembl ENSG00000091140; Homo sapiens. [Contig view]
Phylogenomic databases
HOVERGEN P09622; -.
Other
DrugBank DB00157; NADH.
SOURCE DLD; Homo sapiens.
ProtoNet P09622.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; Acetylation; Disease mutation; FAD; Flavoprotein; Mitochondrion; NAD; Oxidoreductase; Polymorphism; Redox-active center; Transit peptide.
Features
SEVIEWER logo Feature table viewer
KeyFrom   To Length Description FTId
TRANSIT   1    35  35     Mitochondrion. 
CHAIN   36   509  474     Dihydrolipoyl dehydrogenase, mitochondrial. PRO_0000030295
NP_BIND   71    80  10     FAD. 
NP_BIND   183   185  3     FAD. 
NP_BIND   220   227  8     NAD. 
NP_BIND   361   364  4     FAD. 
ACT_SITE   487   487        Proton acceptor (By similarity). 
BINDING   89    89        FAD. 
BINDING   154   154        FAD; via amide nitrogen and carbonyl oxygen. 
BINDING   243   243        NAD. 
BINDING   278   278        NAD; via amide nitrogen and carbonyl oxygen. 
BINDING   314   314        NAD; via amide nitrogen. 
BINDING   355   355        FAD. 
MOD_RES   127   127        N6-acetyllysine (By similarity). 
DISULFID   80    85        Redox-active. 
VARIANT   72    72  1     K -> E (in DLD deficiency). VAR_006907 [3D]
VARIANT   104   104  1     T -> K (in dbSNP:rs1130477 [NCBI]). VAR_031922 [3D]
VARIANT   229   229  1     G -> C (in DLD deficiency; carrier rate among Askenazi Jewish 1:94). VAR_015820 [3D]
VARIANT   331   331  1     L -> V (in dbSNP:rs17624 [NCBI]). VAR_014555 [3D]
VARIANT   488   488  1     P -> L (in DLD deficiency). VAR_006908 [3D]
VARIANT   495   495  1     R -> G (in DLD deficiency; loss of enzyme activity). VAR_015821 [3D]
CONFLICT   154   154        G -> R (in Ref. 2; AAA35764). 
CONFLICT   209   209        L -> F (in Ref. 4; BAD92940). 
CONFLICT   493   493        A -> AEA (in Ref. 3; AAB01381). 
STRAND   40    47  8      
HELIX   51    62  12      
STRAND   67    71  5      
STRAND   73    77  5      
HELIX   78    83  6      
HELIX   85   102  18      
HELIX   105   108  4      
STRAND   111   114  4      
STRAND   116   118  3      
HELIX   120   144  25      
STRAND   148   158  11      
STRAND   161   165  5      
STRAND   171   181  11      
STRAND   185   187  3      
STRAND   197   201  5      
HELIX   203   206  4      
STRAND   214   219  6      
HELIX   223   234  12      
STRAND   238   242  5      
STRAND   244   249  6      
HELIX   255   267  13      
STRAND   271   273  3      
STRAND   275   283  9      
STRAND   289   295  7      
STRAND   302   311  10      
STRAND   315   317  3      
HELIX   324   327  4      
STRAND   350   352  3      
HELIX   354   356  3      
STRAND   357   359  3      
HELIX   363   377  15      
HELIX   386   388  3      
STRAND   391   393  3      
STRAND   395   403  9      
HELIX   406   412  7      
STRAND   416   422  7      
HELIX   423   425  3      
HELIX   427   431  5      
STRAND   438   444  7      
TURN   445   447  3      
STRAND   449   457  9      
HELIX   460   473  14      
HELIX   477   482  6      
HELIX   491   503  13      
Sequence information
Length: 509 AA [This is the length of the unprocessed precursor] Molecular weight: 54150 Da [This is the MW of the unprocessed precursor] CRC64: BD10006B52F4369B [This is a checksum on the sequence]
        10         20         30         40         50         60 
MQSWSRVYCS LAKRGHFNRI SHGLQGLSAV PLRTYADQPI DADVTVIGSG PGGYVAAIKA 

        70         80         90        100        110        120 
AQLGFKTVCI EKNETLGGTC LNVGCIPSKA LLNNSHYYHM AHGTDFASRG IEMSEVRLNL 

       130        140        150        160        170        180 
DKMMEQKSTA VKALTGGIAH LFKQNKVVHV NGYGKITGKN QVTATKADGG TQVIDTKNIL 

       190        200        210        220        230        240 
IATGSEVTPF PGITIDEDTI VSSTGALSLK KVPEKMVVIG AGVIGVELGS VWQRLGADVT 

       250        260        270        280        290        300 
AVEFLGHVGG VGIDMEISKN FQRILQKQGF KFKLNTKVTG ATKKSDGKID VSIEAASGGK 

       310        320        330        340        350        360 
AEVITCDVLL VCIGRRPFTK NLGLEELGIE LDPRGRIPVN TRFQTKIPNI YAIGDVVAGP 

       370        380        390        400        410        420 
MLAHKAEDEG IICVEGMAGG AVHIDYNCVP SVIYTHPEVA WVGKSEEQLK EEGIEYKVGK 

       430        440        450        460        470        480 
FPFAANSRAK TNADTDGMVK ILGQKSTDRV LGAHILGPGA GEMVNEAALA LEYGASCEDI 

       490        500 
ARVCHAHPTL SEAFREANLA ASFGKSINF 

P09622 in FASTA format

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BLAST logo BLAST submission on ExPASy/SIB
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Tools Sequence analysis tools: ProtParam, ProtScale, Compute pI/Mw, PeptideMass,