Human Gene DLD (ENST00000205402.10) from GENCODE V44
  Description: Homo sapiens dihydrolipoamide dehydrogenase (DLD), transcript variant 1, mRNA; nuclear gene for mitochondrial product. (from RefSeq NM_000108)
RefSeq Summary (NM_000108): This gene encodes a member of the class-I pyridine nucleotide-disulfide oxidoreductase family. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. In homodimeric form, the encoded protein functions as a dehydrogenase and is found in several multi-enzyme complexes that regulate energy metabolism. However, as a monomer, this protein can function as a protease. Mutations in this gene have been identified in patients with E3-deficient maple syrup urine disease and lipoamide dehydrogenase deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014].
Gencode Transcript: ENST00000205402.10
Gencode Gene: ENSG00000091140.15
Transcript (Including UTRs)
   Position: hg38 chr7:107,891,183-107,921,198 Size: 30,016 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg38 chr7:107,891,251-107,919,259 Size: 28,009 Coding Exon Count: 14 

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RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:107,891,183-107,921,198)mRNA (may differ from genome)Protein (509 aa)
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-  Comments and Description Text from UniProtKB
  ID: DLDH_HUMAN
DESCRIPTION: RecName: Full=Dihydrolipoyl dehydrogenase, mitochondrial; EC=1.8.1.4; AltName: Full=Dihydrolipoamide dehydrogenase; AltName: Full=Glycine cleavage system L protein; Flags: Precursor;
FUNCTION: Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.
CATALYTIC ACTIVITY: Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(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.
PTM: Tyrosine phosphorylated (By similarity).
DISEASE: Note=Defects in DLD are involved in the development 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.
SEQUENCE CAUTION: Sequence=BAD92940.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/DLD";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DLD
Diseases sorted by gene-association score: dihydrolipoamide dehydrogenase deficiency* (1691), dihydrolipoamide dehydrogenase e3 deficiency* (118), leigh syndrome* (19), retinal degeneration, late-onset, autosomal dominant (12), lactic acidosis (11), cutaneous anthrax (9), alpha-ketoglutarate dehydrogenase deficiency (9), interstitial pneumonitis, desquamative, familial (7), corneal endothelial dystrophy, autosomal recessive (6), maple syrup urine disease, type ii (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.48 RPKM in Heart - Left Ventricle
Total median expression: 914.96 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -17.9068-0.263 Picture PostScript Text
3' UTR -480.501939-0.248 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
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

Pfam Domains:
PF00070 - Pyridine nucleotide-disulphide oxidoreductase
PF07992 - Pyridine nucleotide-disulphide oxidoreductase
PF02852 - Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1ZMC - X-ray MuPIT 1ZMD - X-ray MuPIT 1ZY8 - X-ray MuPIT 2F5Z - X-ray MuPIT 3RNM - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P09622
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
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Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
AlignmentAlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004148 dihydrolipoyl dehydrogenase activity
GO:0005515 protein binding
GO:0009055 electron carrier activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0043544 lipoamide binding
GO:0050660 flavin adenine dinucleotide binding
GO:0051287 NAD binding
GO:0034604 pyruvate dehydrogenase (NAD+) activity

Biological Process:
GO:0006086 acetyl-CoA biosynthetic process from pyruvate
GO:0006103 2-oxoglutarate metabolic process
GO:0006120 mitochondrial electron transport, NADH to ubiquinone
GO:0006508 proteolysis
GO:0007369 gastrulation
GO:0007568 aging
GO:0009106 lipoate metabolic process
GO:0042391 regulation of membrane potential
GO:0045454 cell redox homeostasis
GO:0048240 sperm capacitation
GO:0051068 dihydrolipoamide metabolic process
GO:0055114 oxidation-reduction process
GO:0061732 mitochondrial acetyl-CoA biosynthetic process from pyruvate

Cellular Component:
GO:0001669 acrosomal vesicle
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005929 cilium
GO:0031410 cytoplasmic vesicle
GO:0031514 motile cilium
GO:0042995 cell projection
GO:0043159 acrosomal matrix
GO:0043209 myelin sheath
GO:0045252 oxoglutarate dehydrogenase complex
GO:0045254 pyruvate dehydrogenase complex


-  Descriptions from all associated GenBank mRNAs
  AK294146 - Homo sapiens cDNA FLJ56061 complete cds, highly similar to Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4).
AK312346 - Homo sapiens cDNA, FLJ92665, highly similar to Homo sapiens dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex) (DLD), mRNA.
AK295080 - Homo sapiens cDNA FLJ50515 complete cds, highly similar to Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4).
AK225301 - Homo sapiens mRNA for dihydrolipoamide dehydrogenase precursor variant, clone: HEP01396.
J03490 - Human lipoamide dehydrogenase mRNA, complete cds.
AK297508 - Homo sapiens cDNA FLJ56112 complete cds, highly similar to Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4).
AK300077 - Homo sapiens cDNA FLJ50661 complete cds, highly similar to Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4).
AK225289 - Homo sapiens mRNA for dihydrolipoamide dehydrogenase precursor variant, clone: HEP02468.
AK310220 - Homo sapiens cDNA, FLJ17262.
AB209703 - Homo sapiens mRNA for Dihydrolipoamide dehydrogenase, variant protein.
BC018648 - Homo sapiens dihydrolipoamide dehydrogenase, mRNA (cDNA clone MGC:2115 IMAGE:3029752), complete cds.
BC018696 - Homo sapiens dihydrolipoamide dehydrogenase, mRNA (cDNA clone MGC:3866 IMAGE:3029752), complete cds.
GQ901028 - Homo sapiens clone HEL-T-140 epididymis secretory sperm binding protein mRNA, complete cds.
J03620 - Human dihydrolipoamide dehydrogenase mRNA, complete cds.
JD244949 - Sequence 225973 from Patent EP1572962.
CU676276 - Synthetic construct Homo sapiens gateway clone IMAGE:100023034 5' read DLD mRNA.
AB529125 - Synthetic construct DNA, clone: pF1KB4983, Homo sapiens DLD gene for dihydrolipoamide dehydrogenase, without stop codon, in Flexi system.
HQ447584 - Synthetic construct Homo sapiens clone IMAGE:100070927; CCSB014673_03 dihydrolipoamide dehydrogenase (DLD) gene, encodes complete protein.
KJ891053 - Synthetic construct Homo sapiens clone ccsbBroadEn_00447 DLD gene, encodes complete protein.
KR711447 - Synthetic construct Homo sapiens clone CCSBHm_00023758 DLD (DLD) mRNA, encodes complete protein.
KR711448 - Synthetic construct Homo sapiens clone CCSBHm_00023759 DLD (DLD) mRNA, encodes complete protein.
KR711449 - Synthetic construct Homo sapiens clone CCSBHm_00023761 DLD (DLD) mRNA, encodes complete protein.
KR711450 - Synthetic construct Homo sapiens clone CCSBHm_00023762 DLD (DLD) mRNA, encodes complete protein.
JD020815 - Sequence 1839 from Patent EP1572962.
JD026960 - Sequence 7984 from Patent EP1572962.
JD034878 - Sequence 15902 from Patent EP1572962.
JD025842 - Sequence 6866 from Patent EP1572962.
JD553629 - Sequence 534653 from Patent EP1572962.
JD520760 - Sequence 501784 from Patent EP1572962.
JD557847 - Sequence 538871 from Patent EP1572962.
JD494915 - Sequence 475939 from Patent EP1572962.
JD233779 - Sequence 214803 from Patent EP1572962.
JD141259 - Sequence 122283 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00010 - Glycolysis / Gluconeogenesis
hsa00020 - Citrate cycle (TCA cycle)
hsa00260 - Glycine, serine and threonine metabolism
hsa00280 - Valine, leucine and isoleucine degradation
hsa00620 - Pyruvate metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
GLYCLEAV-PWY - glycine cleavage
ILEUDEG-PWY - L-isoleucine degradation
LEU-DEG2-PWY - L-leucine degradation
PWY-5046 - 2-oxoisovalerate decarboxylation to isobutanoyl-CoA
PWY-5084 - 2-oxoglutarate decarboxylation to succinyl-CoA
PWY-5130 - 2-oxobutanoate degradation
PWY-5328 - superpathway of methionine degradation
PWY66-398 - TCA cycle
PWY66-407 - superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle
PWY66-428 - L-threonine degradation
PYRUVDEHYD-PWY - pyruvate decarboxylation to acetyl CoA
VALDEG-PWY - L-valine degradation

Reactome (by CSHL, EBI, and GO)

Protein P09622 (Reactome details) participates in the following event(s):

R-HSA-5694018 DLD dimer:2xFAD oxidises GCSH:DHLL to GCSH:lipoate
R-HSA-5693148 BCKDK phosphorylates BCKDH
R-HSA-5693153 PPM1K dephosphorylates p-BCKDH
R-HSA-203946 PDK isoforms phosphorylate lipo-PDH
R-HSA-204169 PDP dephosphorylates p-lipo-PDH
R-HSA-6792572 LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs
R-HSA-71037 alpha-ketoadipate + CoASH + NAD+ => glutaryl-CoA + CO2 + NADH + H+
R-HSA-71401 alpha-ketoglutarate + CoASH + NAD+ => succinyl-CoA + CO2 + NADH + H+
R-HSA-70713 BCKDH transfers CoA group from CoA-SH to BCAAs
R-HSA-71397 lipo-PDH decarboxylates PYR to Ac-CoA
R-HSA-6783984 Glycine degradation
R-HSA-70895 Branched-chain amino acid catabolism
R-HSA-204174 Regulation of pyruvate dehydrogenase (PDH) complex
R-HSA-5362517 Signaling by Retinoic Acid
R-HSA-389661 Glyoxylate metabolism and glycine degradation
R-HSA-71064 Lysine catabolism
R-HSA-71403 Citric acid cycle (TCA cycle)
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-70268 Pyruvate metabolism
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-6788656 Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle
R-HSA-1430728 Metabolism
R-HSA-162582 Signal Transduction
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5X0, DLDH_HUMAN, ENST00000205402.1, ENST00000205402.2, ENST00000205402.3, ENST00000205402.4, ENST00000205402.5, ENST00000205402.6, ENST00000205402.7, ENST00000205402.8, ENST00000205402.9, GCSL, LAD, NM_000108, P09622, PHE3, Q14131, Q14167, Q59EV8, Q8WTS4, uc003vet.1, uc003vet.2, uc003vet.3, uc003vet.4, uc003vet.5, uc003vet.6
UCSC ID: ENST00000205402.10
RefSeq Accession: NM_000108
Protein: P09622 (aka DLDH_HUMAN)
CCDS: CCDS5749.1, CCDS78269.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene DLD:
dld-def (Dihydrolipoamide Dehydrogenase Deficiency)
leigh-nucl-ov (Nuclear Gene-Encoded Leigh Syndrome SpectrumOverview)
pdhc-def-ov (Primary Pyruvate Dehydrogenase Complex Deficiency Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.