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Literature summary for 5.6.2.3 extracted from
- Structure, function and evolution of the animal mitochondrial replicative DNA helicase (2016), Crit. Rev. Biochem. Mol. Biol., 51, 53-64 .
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| mitochondrial single-stranded DNA-binding protein | mtSSB, stimulation of dsDNA unwinding by human mtDNA helicase by wild-type mtSSB and several variant forms, targeting amino acid residues that are conserved among mtSSBs, overview. Maximal stimulation of human mtDNA helicase can be achieved both by human mtSSB and non-cognate SSBs including Drosophila melanogaster mtSSB and Escherichia coli SSB, several of the human variants exhibit substantially reduced stimulation. The variants E33A/G34A/K35A in loop 1,2 (according to the nomenclature adopted for Escherichia coli SSB) and Y100A/G101A/E102A in loop 4,5-2 show an about 40% reduced stimulation, while DS51-L59 in loop 2,3 shows a 15% reduction. Specific functional and perhaps physical interactions facilitate dsDNA unwinding by human mtDNA helicase | Homo sapiens |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene Dmel_CG5924, sequence comparisons | Drosophila melanogaster |
| gene Twinkle, sequence comparisons | Mus musculus |
| gene Twinkle, sequence comparisons, recombinant overexpression in HEK-293 cells | Homo sapiens |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| A326T | site-directed mutagenesis | Drosophila melanogaster |
| A359T | naturally occurring mutation in the linker region or CTD of the human enzyme | Homo sapiens |
| A442P | site-directed mutagenesis, the catalytic mutant shows a lethal phenotype and and mtDNA depletion | Drosophila melanogaster |
| F485L | naturally occurring mutation in the linker region or CTD of the human enzyme | Homo sapiens |
| I334P | site-directed mutagenesis, the catalytic mutant shows a lethal phenotype and mtDNA depletion | Drosophila melanogaster |
| L381P | naturally occurring mutation in the linker region or CTD of the human enzyme | Homo sapiens |
| additional information | ATP-dependent DNA unwinding increases about 50% with the overexpression of full-length enzyme from Twinkle gene in HEK-293 cells. The C-terminal region of human mtDNA helicase that is removed in T66 (66 kDa variant) represents an extension relative to the T7 gp4 polypeptide, and the further N-terminal deletion in T57 (57 kDA variant) at position K144 is consistent with the removal of the N-terminal zinc-binding domain (ZBD) in T7 gp4. An NTD only construct (DELTA372-684) shows no ATPase activity | Homo sapiens |
| additional information | mtDNA helicase overexpression and knockdown, overexpression increases mtDNA copy number about 1.4fold while knockdown by RNA interference results in about 5fold decrease in mtDNA. Catalytic mutants analogous to A318 and D424 in the Walker A and B motifs in the helicase domain of T7 gp4, respectively, generate a dominant-negative, lethal phenotype resulting from a dramatic mtDNA depletion of 14-20fold. Mitochondrial transcript levels are reduced as a consequence of mtDNA depletion, but only after a 2fold decrease in mtDNA copy number is incurred. Overexpression of variants carrying analogous human-disease alleles in either the linker or C-terminal domain show differential effects. All are able to form hexamers in vivo, the I334P and A442P mutants (I367T and A475P in humans) show the lethal phenotype and mtDNA depletion found for the catalytic mutants, while A326T, R341Q, and W441C (A359T, R734Q, and W474C in humans) do not. Construction and evaluation of N-terminal domain-only variants of the Drosophila melanogaster homologue of human mtDNA helicase, the full-length NTD and its truncation variants in recombinant form are ssDNA-binding monomers | Drosophila melanogaster |
| R341Q | site-directed mutagenesis | Drosophila melanogaster |
| S369P | naturally occurring mutation in the linker region or CTD of the human enzyme | Homo sapiens |
| W441C | site-directed mutagenesis | Drosophila melanogaster |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| ssDNA | the ssDNA annealing activity opposes the dsDNA unwinding activity of mtDNA helicase in the absence of an SSB or a ssDNA trap, and only ssDNA but not dsDNA serves as a competitive inhibitor of annealing activity even though the helicase is shown to bind dsDNA | Drosophila melanogaster |  |
| ssDNA | the ssDNA annealing activity opposes the dsDNA unwinding activity of human mtDNA helicase in the absence of an SSB or a ssDNA trap, and only ssDNA but not dsDNA serves as a competitive inhibitor of annealing activity even though the helicase is shown to bind dsDNA | Homo sapiens | |
| ssDNA | the ssDNA annealing activity opposes the dsDNA unwinding activity of human mtDNA helicase in the absence of an SSB or a ssDNA trap, and only ssDNA but not dsDNA serves as a competitive inhibitor of annealing activity even though the helicase is shown to bind dsDNA | Mus musculus | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| mitochondrion | - |
Homo sapiens | 5739 | - |
| mitochondrion | - |
Drosophila melanogaster | 5739 | - |
| mitochondrion | - |
Mus musculus | 5739 | - |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Homo sapiens | |
| Mg2+ | required | Drosophila melanogaster | |
| Mg2+ | required | Mus musculus | |
| Zn2+ | the enzyme contains a zinc binding-like domain (ZBD) | Homo sapiens | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 420000 | - |
velocity sedimentation and gel filtration | Homo sapiens |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + H2O | Homo sapiens | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Drosophila melanogaster | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Mus musculus | - |
ADP + phosphate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Drosophila melanogaster | Q9VL76 | - |
- |
| Homo sapiens | Q96RR1 | - |
- |
| Mus musculus | Q8CIW5 | - |
- |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| heart | - |
Homo sapiens | - |
| HEK-293 cell | - |
Homo sapiens | - |
| SCHNEIDER-2 cell | - |
Drosophila melanogaster | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + H2O | - |
Homo sapiens | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Drosophila melanogaster | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Mus musculus | ADP + phosphate | - |
? | |
| additional information | three catalytic activities are ascribed to the recombinant human mtDNA helicase: DNA-dependent NTPase, 5'-3' dsDNA unwinding, and nucleotide-independent ssDNA annealing. DNA primase activity associated with the N-terminal half of the T7 gp4 primase-helicase has not been found. DNA unwinding assay on oligonucleotide substrates, the DNA-dependent ATPase assay, several DNA binding assays and the replisome assay are employed | Homo sapiens | ? | - |
- |
|
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| hexamer | 6 * 72000, SDS-PAGE | Homo sapiens |
| More | modular nature of a recombinant form of the human mitochondrial DNA (mtDNA) helicase. Under conditions of high ionic strength mtDNA helicase forms hexamers and heptamers, the proportion of which is shifted, at low ionic strength, toward the heptameric state in the presence of Mg2+ and ATPgammaS. Limited proteolysis with trypsin demonstrated that binding of ATP produces a conformational change that is distinct from that in the presence of ADP. Domain model of the human mtDNA helicase, and heptameric three-dimensional structure model, overview. Modelling of the RPD domain | Homo sapiens |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| Dmel_CG5924 | - |
Drosophila melanogaster |
| mitochondrial DNA helicase | - |
Homo sapiens |
| mitochondrial replicative DNA helicase | - |
Homo sapiens |
| mitochondrial replicative DNA helicase | - |
Drosophila melanogaster |
| mitochondrial replicative DNA helicase | - |
Mus musculus |
| mtDNA helicase | - |
Homo sapiens |
| mtDNA helicase | - |
Drosophila melanogaster |
| mtDNA helicase | - |
Mus musculus |
| replicative mtDNA helicase | - |
Homo sapiens |
| replicative mtDNA helicase | - |
Drosophila melanogaster |
| replicative mtDNA helicase | - |
Mus musculus |
| TWINKLE | - |
Homo sapiens |
| TWINKLE | - |
Mus musculus |
| TWNK | - |
Homo sapiens |
| TWNK | - |
Mus musculus |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | an NTD only construct (DELTA372-684) shows no ATPase activity. Several naturally occurring mutations in the enzyme sequence are determinated, e.g. pathogenic mutations in the linker region and CTD in that affect the functional organization | Homo sapiens |
| malfunction | mutations in Drosophila melanogaster mtDNA helicase analogously to mutations found in human patients result in severe mtDNA depletion in S2 cells, whereas alanine-substitutions of the amino acids that are conserved in prokaryotic RPDs have no effect on mtDNA copy number | Drosophila melanogaster |
| additional information | structure comparisons of human, mouse, and Drosophila melanogaster enzymes, modular architecture, overview. Modeling of the C-terminal domain of Drosophila melanogaster mtDNA helicase also provides a structure that resembles the homologous domain of all the DNA helicases mentioned. Modelling of the RPD domain | Drosophila melanogaster |
| additional information | structure comparisons of human, mouse, and Drosophila melanogaster enzymes, modular architecture, overview. Modelling of the RPD domain | Mus musculus |
| additional information | structure comparisons of human, mouse, and Drosophila melanogaster enzymes, modular architecture, overview. Structural model for the RNA polymerase-like domain (RPD) of human mtDNA helicase, overview. In the C-terminal half of the NTD of human mtDNA helicase, the RPD adopts a conformation comprising two subdomains: an N-terminal region and a TOPRIM fold | Homo sapiens |
| physiological function | DNA helicases are essential components of the DNA replication, repair and recombination machinery across taxa. The replicative DNA helicases are members of the AAA+ family of ATPases and contain a conserved alpha-beta core structure domain that carries the conserved amino acid sequence motifs required for nucleotide hydrolysis. The ssDNA annealing activity might be involved in recombination-mediated replication, a mtDNA replication mechanism supported by physiological studies of mtDNA replication intermediates from human heart, or possibly in replication fork regression during DNA repair as has been described in prokaryotic and nuclear genomes | Drosophila melanogaster |
| physiological function | DNA helicases are essential components of the DNA replication, repair and recombination machinery across taxa. The replicative DNA helicases are members of the AAA+ family of ATPases and contain a conserved alpha-beta core structure domain that carries the conserved amino acid sequence motifs required for nucleotide hydrolysis. The ssDNA annealing activity opposes the dsDNA unwinding activity of human mtDNA helicase in the absence of an SSB or a ssDNA trap, and only ssDNA but not dsDNA serves as a competitive inhibitor of annealing activity even though the helicase is shown to bind dsDNA. The ssDNA annealing activity might be involved in recombination-mediated replication, a mtDNA replication mechanism supported by physiological studies of mtDNA replication intermediates from human heart, or possibly in replication fork regression during DNA repair as has been described in prokaryotic and nuclear genomes | Mus musculus |
| physiological function | DNA helicases are essential components of the DNA replication, repair and recombination machinery across taxa. The replicative DNA helicases are members of the AAA+ family of ATPases and contain a conserved alpha-beta core structure domain that carries the conserved amino acid sequence motifs required for nucleotide hydrolysis. The ssDNA annealing activity opposes the dsDNA unwinding activity of human mtDNA helicase in the absence of an SSB or a ssDNA trap, and only ssDNA but not dsDNA serves as a competitive inhibitor of annealing activity even though the helicase is shown to bind dsDNA. The ssDNA annealing activity might be involved in recombination-mediated replication, a mtDNA replication mechanism supported by physiological studies of mtDNA replication intermediates from human heart, or possibly in replication fork regression during DNA repair as has been described in prokaryotic and nuclear genomes. Importance of the enzyme for mitochondrial function and human health | Homo sapiens |
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