E3 binding protein

Last updated
PDHX
PDB 1zy8 EBI.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases PDHX , DLDBP, E3BP, OPDX, PDX1, proX, pyruvate dehydrogenase complex component X, PDHXD
External IDs OMIM: 608769; MGI: 1351627; HomoloGene: 55757; GeneCards: PDHX; OMA:PDHX - orthologs
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001135024
NM_001166158
NM_003477

NM_175094

RefSeq (protein)

NP_001128496
NP_001159630
NP_003468

NP_780303

Location (UCSC) Chr 11: 34.92 – 35.02 Mb Chr 2: 102.85 – 102.9 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

E3 binding protein also known as pyruvate dehydrogenase protein X component, mitochondrial is a protein that in humans is encoded by the PDHX gene. [5] [6] [7] [8] The E3 binding protein is a component of the pyruvate dehydrogenase complex found only in eukaryotes. Defects in this gene are a cause of pyruvate dehydrogenase deficiency which results in neurological dysfunction and lactic acidosis in infancy and early childhood. This protein is also a minor antigen for antimitochondrial antibodies. These autoantibodies are present in nearly 95% of patients with primary biliary cholangitis, an autoimmune disease of the liver. In primary biliary cholangitis, activated T lymphocytes attack and destroy epithelial cells in the bile duct where this protein is abnormally distributed and overexpressed. Primary biliary cholangitis eventually leads to liver failure. [5]

Contents

Structure

The mRNA encoded by the human PDHX gene is approximately 2.5 kb in length, and expressed primarily in human skeletal and cardiac muscle tissues. The gene has been localized in humans to the 11th chromosome, with the specific location being 11p1.3. [9]

The protein encoded by the human PDHX gene, also known as E3 binding protein (E3BP), is part of the pyruvate dehydrogenase complex, a required complex for cellular respiration that catalyzes the dehydration of pyruvate to Acetyl-CoA. [10] The entire complex is 9.5 MDa in size, and has been described as 60-meric, meaning there are over 60 components that are assembled to make the entire complex. These subunits are conserved across many species, as the function of this complex is essential for the generation of ATP for all eukaryotes. The E3 binding protein directly interacts with the dihydrolipoamide transacetylase (E2) core, anchoring it to the complex. E3BP binds the I domain of E2 by its C-terminal I' domain. The composition of E2.E3BP was thought to be 60 E2 plus approximately 12 E3BP, however, equilibrium sedimentation and small angle x-ray scattering studies showed that the E3BP/E2 binding complex has a lower mass than the E2 subunit alone. Additionally, these studies showed that E3 binds to E2.E3BP outside the central dodecahedron of the PDH complex, and that this interaction creates a lower binding affinity for the E1 subunit. Together, these data support a substitution model, in which the smaller E3BP subunits replace the E2 subunits rather than adding to the 60-mer entire complex. The specific model illustrates 12 I domains of E2 being substituted by 12 I' domains of E3BP, thereby forming 6 dimer edges that are symmetrically located in the dodecahedron structure. [11]

E3BP similarly binds to E3, having linker regions that connect an E3-binding domain and a lipoyl domain. [11] Crystallography of the complex has shown that, E3BD also binds to E3, though no significant conformational changes occur. In this binding, two E3 subunits come together to form the binding site. [12] This has also shown that E3BP has residues that come into contact with the E3 component across its two-fold axis; this means that there is one binding site for this reaction on the E3 homodimer. Changing the central residues at the E3BD/E3 interface affect binding much more drastically than does changing peripheral residues. This data corroborates the theory of the existence of a “hot spot”. [13] Specifically, there are three hydrophobic residues within the binding domain of E3BP - Pro133, Pro154, and Ile157 – that interact with the surface of both E3 polypeptide chains. This interaction is significantly stabilized by many ionic and hydrogen bonds that take place between the residues of three interacting polypeptide chains adjacent to the central hydrophobic patch. This specificity is most likely due to the lack of conformational flexibility of the binding fragment of E3BP and the complementary amino acid match with the E3 interface. [12]

Function

The pyruvate dehydrogenase (PDH) complex is located in the mitochondrial matrix and catalyzes the conversion of pyruvate to acetyl coenzyme A. The PDH complex thereby links glycolysis to the citric acid cycle. The PDH complex contains three catalytic subunits, E1, E2, and E3, two regulatory subunits, E1 kinase and E1 phosphatase, and a non-catalytic subunit, E3 binding protein (E3BP). This gene encodes the E3 binding protein subunit; also known as component X of the pyruvate dehydrogenase complex. This protein tethers E3 dimers to the E2 core of the PDH complex. [5]

Clinical significance

Mutations in the PDHX gene have been known to cause one form of pyruvate dehydrogenase deficiency. Pyruvate dehydrogenase deficiency is characterized by the buildup of a chemical called lactic acid in the body and a variety of neurological problems. Signs and symptoms of this condition usually first appear shortly after birth, and they can vary widely among affected individuals. The most common feature is a potentially life-threatening buildup of lactic acid (lactic acidosis), which can cause nausea, vomiting, severe breathing problems, and an abnormal heartbeat. People with pyruvate dehydrogenase deficiency usually have neurological problems as well. Most have delayed development of mental abilities and motor skills such as sitting and walking. Other neurological problems can include intellectual disability, seizures, weak muscle tone (hypotonia), poor coordination, and difficulty walking. Some affected individuals have abnormal brain structures, such as underdevelopment of the tissue connecting the left and right halves of the brain (corpus callosum), wasting away (atrophy) of the exterior part of the brain known as the cerebral cortex, or patches of damaged tissue (lesions) on some parts of the brain. Because of the severe health effects, many individuals with pyruvate dehydrogenase deficiency do not survive past childhood, although some may live into adolescence or adulthood. [5]

While this deficiency primarily results in mutations in the E1 alpha subunit of the PDH complex, a few mutations have been identified in the PDX1 gene. [14] Specific investigations of this gene have identified 78del85 and 965del59 mutations in a homozygous state, while some mutations could not be identified due to no PDHX mRNA being expressed in the individuals. [9] [15] In other cases, it has been reported that an entire exon, exon 10, was removed due to a gross deletion mutation; the mechanism for this has been theorized to be a mispairing, because there is an exact direct repeat, CCACTG, within the gene. [16] Other large deletions (over 3900 bp) have been reported. [17] E3BP, in coordination with the E2 subunit, has also been shown to be a secondary antigen for antimitochondrial antibodies and immune responses. The autoantibodies for this protein are present in the vast majority of patients with primary biliary cirrhosis, a chronic, progressive cholestatic liver disease that usually affects middle-aged women and eventually leads to liver failure. [5] [18]

Interactive pathway map

Click on genes, proteins and metabolites below to link to respective articles. [§ 1]

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WP534.png go to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to articlego to WikiPathwaysgo to articlego to Entrezgo to article
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Glycolysis and Gluconeogenesis edit
  1. The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534".

Related Research Articles

<span class="mw-page-title-main">Pyruvate dehydrogenase complex</span> Three-enzyme complex

Pyruvate dehydrogenase complex (PDC) is a complex of three enzymes that converts pyruvate into acetyl-CoA by a process called pyruvate decarboxylation. Acetyl-CoA may then be used in the citric acid cycle to carry out cellular respiration, and this complex links the glycolysis metabolic pathway to the citric acid cycle. Pyruvate decarboxylation is also known as the "pyruvate dehydrogenase reaction" because it also involves the oxidation of pyruvate.

<span class="mw-page-title-main">Leigh syndrome</span> Metabolic disease

Leigh syndrome is an inherited neurometabolic disorder that affects the central nervous system. It is named after Archibald Denis Leigh, a British neuropsychiatrist who first described the condition in 1951. Normal levels of thiamine, thiamine monophosphate, and thiamine diphosphate are commonly found, but there is a reduced or absent level of thiamine triphosphate. This is thought to be caused by a blockage in the enzyme thiamine-diphosphate kinase, and therefore treatment in some patients would be to take thiamine triphosphate daily. While the majority of patients typically exhibit symptoms between the ages of 3 and 12 months, instances of adult onset have also been documented.

<span class="mw-page-title-main">Pyruvate dehydrogenase lipoamide kinase isozyme 1</span> Protein-coding gene in the species Homo sapiens

Pyruvate dehydrogenase lipoamide kinase isozyme 1, mitochondrial is an enzyme that in humans is encoded by the PDK1 gene. It codes for an isozyme of pyruvate dehydrogenase kinase (PDK).

The branched-chain α-ketoacid dehydrogenase complex is a multi-subunit complex of enzymes that is found on the mitochondrial inner membrane. This enzyme complex catalyzes the oxidative decarboxylation of branched, short-chain alpha-ketoacids. BCKDC is a member of the mitochondrial α-ketoacid dehydrogenase complex family, which also includes pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, key enzymes that function in the Krebs cycle.

Pyruvate dehydrogenase deficiency is a rare neurodegenerative disorder associated with abnormal mitochondrial metabolism. PDCD is a genetic disease resulting from mutations in one of the components of the pyruvate dehydrogenase complex (PDC). The PDC is a multi-enzyme complex that plays a vital role as a key regulatory step in the central pathways of energy metabolism in the mitochondria. The disorder shows heterogeneous characteristics in both clinical presentation and biochemical abnormality.

<span class="mw-page-title-main">Dihydrolipoyl transacetylase</span> Enzyme

Dihydrolipoyl transacetylase is an enzyme component of the multienzyme pyruvate dehydrogenase complex. The pyruvate dehydrogenase complex is responsible for the pyruvate decarboxylation step that links glycolysis to the citric acid cycle. This involves the transformation of pyruvate from glycolysis into acetyl-CoA which is then used in the citric acid cycle to carry out cellular respiration.

Oxidative decarboxylation is a decarboxylation reaction caused by oxidation. Most are accompanied by α- Ketoglutarate α- Decarboxylation caused by dehydrogenation of hydroxyl carboxylic acids such as carbonyl carboxylic acid, malic acid, isocitric acid, etc.

<span class="mw-page-title-main">Pyruvate dehydrogenase</span> Class of enzymes

Pyruvate dehydrogenase is an enzyme that catalyzes the reaction of pyruvate and a lipoamide to give the acetylated dihydrolipoamide and carbon dioxide. The conversion requires the coenzyme thiamine pyrophosphate.

<span class="mw-page-title-main">Dihydrolipoamide dehydrogenase</span> Protein-coding gene in the species Homo sapiens

Dihydrolipoamide dehydrogenase (DLD), also known as dihydrolipoyl dehydrogenase, mitochondrial, is an enzyme that in humans is encoded by the DLD gene. DLD is a flavoprotein enzyme that oxidizes dihydrolipoamide to lipoamide.

<span class="mw-page-title-main">Pyruvate dehydrogenase phosphatase</span> Protein-coding gene in the species Homo sapiens

Pyruvate dehydrogenase phosphatase catalytic subunit 1, also known as protein phosphatase 2C, is an enzyme that in humans is encoded by the PDP1 gene. PDPC 1 is an enzyme which serves to reverse the effects of pyruvate dehydrogenase kinase upon pyruvate dehydrogenase, activating pyruvate dehydrogenase.

<span class="mw-page-title-main">Pyruvate dehydrogenase (lipoamide) alpha 1</span> Protein-coding gene in the species Homo sapiens

Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial is an enzyme that in humans is encoded by the PDHA1 gene.The pyruvate dehydrogenase complex is a nuclear-encoded mitochondrial matrix multienzyme complex that provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle by catalyzing the irreversible conversion of pyruvate into acetyl-CoA. The PDH complex is composed of multiple copies of 3 enzymes: E1 (PDHA1); dihydrolipoyl transacetylase (DLAT) ; and dihydrolipoyl dehydrogenase (DLD). The E1 enzyme is a heterotetramer of 2 alpha and 2 beta subunits. The E1-alpha subunit contains the E1 active site and plays a key role in the function of the PDH complex.

<span class="mw-page-title-main">Lactate dehydrogenase</span> Class of enzymes

Lactate dehydrogenase (LDH or LD) is an enzyme found in nearly all living cells. LDH catalyzes the conversion of pyruvate to lactate and back, as it converts NAD+ to NADH and back. A dehydrogenase is an enzyme that transfers a hydride from one molecule to another.

<span class="mw-page-title-main">BCKDHA</span> Protein-coding gene in the species Homo sapiens

A 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial is an enzyme that in humans is encoded by the BCKDHA gene.

<span class="mw-page-title-main">PDK2</span> Protein-coding gene in the species Homo sapiens

Pyruvate dehydrogenase kinase isoform 2 (PDK2) also known as pyruvate dehydrogenase lipoamide kinase isozyme 2, mitochondrial is an enzyme that in humans is encoded by the PDK2 gene. PDK2 is an isozyme of pyruvate dehydrogenase kinase.

<span class="mw-page-title-main">DLST</span> Protein-coding gene in the species Homo sapiens

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial is an enzyme that in humans is encoded by the DLST gene.

<span class="mw-page-title-main">BCKDHB</span> Protein-coding gene in the species Homo sapiens

2-Oxoisovalerate dehydrogenase subunit beta, mitochondrial is an enzyme that in humans is encoded by the BCKDHB gene.

<span class="mw-page-title-main">PDK3</span> Protein-coding gene in the species Homo sapiens

Pyruvate dehydrogenase lipoamide kinase isozyme 3, mitochondrial is an enzyme that in humans is encoded by the PDK3 gene. It codes for an isozyme of pyruvate dehydrogenase kinase.The pyruvate dehydrogenase (PDH) complex is a nuclear-encoded mitochondrial multienzyme complex that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2. It provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle, and thus is one of the major enzymes responsible for the regulation of glucose metabolism. The enzymatic activity of PDH is regulated by a phosphorylation/dephosphorylation cycle, and phosphorylation results in inactivation of PDH. The protein encoded by this gene is one of the four pyruvate dehydrogenase kinases that inhibits the PDH complex by phosphorylation of the E1 alpha subunit. This gene is predominantly expressed in the heart and skeletal muscles. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

<span class="mw-page-title-main">OGDH</span> Enzyme involved in Krebs cycle

Alpha-ketoglutarate dehydrogenase also known as 2-oxoglutarate dehydrogenase E1 component, mitochondrial is an enzyme that in humans is encoded by the OGDH gene.

<span class="mw-page-title-main">Pyruvate dehydrogenase (lipoamide) alpha 2</span> Protein-coding gene in the species Homo sapiens

Pyruvate dehydrogenase (lipoamide) alpha 2, also known as pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial or PDHE1-A type II, is an enzyme that in humans is encoded by the PDHA2 gene.

<span class="mw-page-title-main">Pyruvate dehydrogenase (lipoamide) beta</span> Protein-coding gene in the species Homo sapiens

Pyruvate dehydrogenase (lipoamide) beta, also known as pyruvate dehydrogenase E1 component subunit beta, mitochondrial or PDHE1-B is an enzyme that in humans is encoded by the PDHB gene. The pyruvate dehydrogenase (PDH) complex is a nuclear-encoded mitochondrial multienzyme complex that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2, and provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle. The PDH complex is composed of multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). The E1 enzyme is a heterotetramer of two alpha and two beta subunits. This gene encodes the E1 beta subunit. Mutations in this gene are associated with pyruvate dehydrogenase E1-beta deficiency.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000110435 Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000010914 Ensembl, May 2017
  3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. 1 2 3 4 5 "Entrez Gene: pyruvate dehydrogenase complex".
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  7. Ling M, McEachern G, Seyda A, MacKay N, Scherer SW, Bratinova S, Beatty B, Giovannucci-Uzielli ML, Robinson BH (Mar 1998). "Detection of a homozygous four base pair deletion in the protein X gene in a case of pyruvate dehydrogenase complex deficiency". Human Molecular Genetics. 7 (3): 501–5. doi: 10.1093/hmg/7.3.501 . PMID   9467010.
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  14. Brown RM, Head RA, Morris AA, Raiman JA, Walter JH, Whitehouse WP, Brown GK (Sep 2006). "Pyruvate dehydrogenase E3 binding protein (protein X) deficiency". Developmental Medicine and Child Neurology. 48 (9): 756–60. doi:10.1017/S0012162206001617 (inactive 2024-06-08). PMID   16904023.{{cite journal}}: CS1 maint: DOI inactive as of June 2024 (link)
  15. Ling M, McEachern G, Seyda A, MacKay N, Scherer SW, Bratinova S, Beatty B, Giovannucci-Uzielli ML, Robinson BH (Mar 1998). "Detection of a homozygous four base pair deletion in the protein X gene in a case of pyruvate dehydrogenase complex deficiency". Human Molecular Genetics. 7 (3): 501–5. doi: 10.1093/hmg/7.3.501 . PMID   9467010.
  16. Miné M, Brivet M, Schiff M, de Baulny HO, Chuzhanova N, Marsac C (2006). "A novel gross deletion caused by non-homologous recombination of the PDHX gene in a patient with pyruvate dehydrogenase deficiency". Molecular Genetics and Metabolism. 89 (1–2): 106–10. doi:10.1016/j.ymgme.2006.06.002. PMID   16843025.
  17. Schiff M, Miné M, Brivet M, Marsac C, Elmaleh-Bergés M, Evrard P, Ogier de Baulny H (Apr 2006). "Leigh's disease due to a new mutation in the PDHX gene". Annals of Neurology. 59 (4): 709–14. doi:10.1002/ana.20818. PMID   16566017. S2CID   43132798.
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Further reading

This article incorporates text from the United States National Library of Medicine, which is in the public domain.