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Literature summary for 5.6.2.4 extracted from
- Grip it and rip it: structural mechanisms of DNA helicase substrate binding and unwinding (2014), Protein Sci., 23, 1498-1507.
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure analysis of the helicase domain from the SF1A DNA helicase PcrA bound to partial-duplex DNA, PDB ID 3PJR | Geobacillus stearothermophilus |
| crystal structure analysis of the helicase domain from the SF2A DNA helicase BLM bound to partial-duplex DNA, PDB ID 4O3M, and structure PDB ID 4CGZ | Homo sapiens |
| crystal structure analysis, PDB ID 2IS1 | Escherichia coli |
| crystal structure analysis, PDB ID 2P6R | Archaeoglobus fulgidus |
| crystal structure analysis, PDB ID 2WWY | Homo sapiens |
| crystal structure analysis, PDB ID 3U44 | Bacillus subtilis |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Escherichia coli |  |
| Mg2+ | required | Homo sapiens | |
| Mg2+ | required | Geobacillus stearothermophilus | |
| Mg2+ | required | Archaeoglobus fulgidus | |
| Mg2+ | required | Bacillus subtilis | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + H2O | Escherichia coli | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Homo sapiens | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Geobacillus stearothermophilus | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Archaeoglobus fulgidus | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Bacillus subtilis | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Bacillus subtilis 168 | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Archaeoglobus fulgidus ATCC 49558 | - |
ADP + phosphate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Archaeoglobus fulgidus | P0DMI1 | - |
- |
| Archaeoglobus fulgidus ATCC 49558 | P0DMI1 | - |
- |
| Bacillus subtilis | P23478 | - |
- |
| Bacillus subtilis 168 | P23478 | - |
- |
| Escherichia coli | P03018 | - |
- |
| Geobacillus stearothermophilus | P56255 | - |
- |
| Homo sapiens | P46063 | - |
- |
| Homo sapiens | P54132 | - |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + H2O | - |
Escherichia coli | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Homo sapiens | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Geobacillus stearothermophilus | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Archaeoglobus fulgidus | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Bacillus subtilis | ADP + phosphate | - |
? | |
| ATP + H2O | the SF1A helicase shows direct DNA binding by conserved aromatic (Trp or Phe) and electropositive (Arg) residues within the ARLs via stacking with ssDNA bases and gripping the phosphodiester backbone, respectively | Escherichia coli | ADP + phosphate | - |
? | |
| ATP + H2O | the SF1A helicase shows direct DNA binding by conserved aromatic (Trp or Phe) and electropositive (Arg) residues within the ARLs via stacking with ssDNA bases and gripping the phosphodiester backbone, respectively | Geobacillus stearothermophilus | ADP + phosphate | - |
? | |
| ATP + H2O | the SF1A helicase shows direct DNA binding by conserved aromatic (Trp or Phe) and electropositive (Arg) residues within the ARLs via stacking with ssDNA bases and gripping the phosphodiester backbone, respectively | Bacillus subtilis | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Bacillus subtilis 168 | ADP + phosphate | - |
? | |
| ATP + H2O | the SF1A helicase shows direct DNA binding by conserved aromatic (Trp or Phe) and electropositive (Arg) residues within the ARLs via stacking with ssDNA bases and gripping the phosphodiester backbone, respectively | Bacillus subtilis 168 | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Archaeoglobus fulgidus ATCC 49558 | ADP + phosphate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | structure-function relationship | Escherichia coli |
| More | structure-function relationship | Homo sapiens |
| More | structure-function relationship | Geobacillus stearothermophilus |
| More | structure-function relationship | Archaeoglobus fulgidus |
| More | structure-function relationship | Bacillus subtilis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| AddA | - |
Bacillus subtilis |
| ATP-dependent DNA helicase Q1 | - |
Homo sapiens |
| ATP-dependent helicase/nuclease subunit A | - |
Bacillus subtilis |
| BLM | - |
Homo sapiens |
| Bloom syndrome protein | - |
Homo sapiens |
| DNA helicase II | - |
Escherichia coli |
| Hel308 | - |
Archaeoglobus fulgidus |
| PcrA | - |
Geobacillus stearothermophilus |
| RecQ1 | - |
Homo sapiens |
| SF1 helicase | - |
Escherichia coli |
| SF1 helicase | - |
Geobacillus stearothermophilus |
| SF1 helicase | - |
Bacillus subtilis |
| SF2 helicase | - |
Homo sapiens |
| SF2 helicase | - |
Archaeoglobus fulgidus |
| UvrD | - |
Escherichia coli |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | superfamilies 1 and 2 (SF1 and SF2) comprise the largest number of helicase families and members are involved in a wide array of cellular functions that require manipulation of DNA or RNA structures, the helicases belong to the AAA+ ATPases. Helicase superfamilies can also be subdivided into those that translocate along DNA and unwind in a 3'-5' direction, e.g., SF1A, or a 5'-3 direction, e.g., SF1B. SF1 and SF2 helicases can be identified based on evolutionary conservation of seven sequence motifs (I, Ia, II-VI) that are required for ATP binding/hydrolysis, nucleic acid binding, and/or translocation. SF1 and SF2 helicases include a conserved core helicase domain that is comprised of two subdomains that share similarity with RecA ATPase/recombinase enzyme family | Escherichia coli |
| evolution | superfamilies 1 and 2 (SF1 and SF2) comprise the largest number of helicase families and members are involved in a wide array of cellular functions that require manipulation of DNA or RNA structures, the helicases belong to the AAA+ ATPases. Helicase superfamilies can also be subdivided into those that translocate along DNA and unwind in a 3'-5' direction, e.g., SF1A, or a 5'-3 direction, e.g., SF1B. SF1 and SF2 helicases can be identified based on evolutionary conservation of seven sequence motifs (I, Ia, II-VI) that are required for ATP binding/hydrolysis, nucleic acid binding, and/or translocation. SF1 and SF2 helicases include a conserved core helicase domain that is comprised of two subdomains that share similarity with RecA ATPase/recombinase enzyme family | Homo sapiens |
| evolution | superfamilies 1 and 2 (SF1 and SF2) comprise the largest number of helicase families and members are involved in a wide array of cellular functions that require manipulation of DNA or RNA structures, the helicases belong to the AAA+ ATPases. Helicase superfamilies can also be subdivided into those that translocate along DNA and unwind in a 3'-5' direction, e.g., SF1A, or a 5'-3 direction, e.g., SF1B. SF1 and SF2 helicases can be identified based on evolutionary conservation of seven sequence motifs (I, Ia, II-VI) that are required for ATP binding/hydrolysis, nucleic acid binding, and/or translocation. SF1 and SF2 helicases include a conserved core helicase domain that is comprised of two subdomains that share similarity with RecA ATPase/recombinase enzyme family | Geobacillus stearothermophilus |
| evolution | superfamilies 1 and 2 (SF1 and SF2) comprise the largest number of helicase families and members are involved in a wide array of cellular functions that require manipulation of DNA or RNA structures, the helicases belong to the AAA+ ATPases. Helicase superfamilies can also be subdivided into those that translocate along DNA and unwind in a 3'-5' direction, e.g., SF1A, or a 5'-3 direction, e.g., SF1B. SF1 and SF2 helicases can be identified based on evolutionary conservation of seven sequence motifs (I, Ia, II-VI) that are required for ATP binding/hydrolysis, nucleic acid binding, and/or translocation. SF1 and SF2 helicases include a conserved core helicase domain that is comprised of two subdomains that share similarity with RecA ATPase/recombinase enzyme family | Archaeoglobus fulgidus |
| evolution | superfamilies 1 and 2 (SF1 and SF2) comprise the largest number of helicase families and members are involved in a wide array of cellular functions that require manipulation of DNA or RNA structures, the helicases belong to the AAA+ ATPases. Helicase superfamilies can also be subdivided into those that translocate along DNA and unwind in a 3'-5' direction, e.g., SF1A, or a 5'-3 direction, e.g., SF1B. SF1 and SF2 helicases can be identified based on evolutionary conservation of seven sequence motifs (I, Ia, II-VI) that are required for ATP binding/hydrolysis, nucleic acid binding, and/or translocation. SF1 and SF2 helicases include a conserved core helicase domain that is comprised of two subdomains that share similarity with RecA ATPase/recombinase enzyme family | Bacillus subtilis |
| additional information | structure comparisons of SF1 and SF2 helicases, SF1 and SF2 helicase domains structures and substrate-bound SF1 and SF2 helicase structures, structure-function relationship, overview | Escherichia coli |
| additional information | structure comparisons of SF1 and SF2 helicases, SF1 and SF2 helicase domains structures and substrate-bound SF1 and SF2 helicase structures, structure-function relationship, overview | Homo sapiens |
| additional information | structure comparisons of SF1 and SF2 helicases, SF1 and SF2 helicase domains structures and substrate-bound SF1 and SF2 helicase structures, structure-function relationship, overview | Geobacillus stearothermophilus |
| additional information | structure comparisons of SF1 and SF2 helicases, SF1 and SF2 helicase domains structures and substrate-bound SF1 and SF2 helicase structures, structure-function relationship, overview | Archaeoglobus fulgidus |
| additional information | structure comparisons of SF1 and SF2 helicases, SF1 and SF2 helicase domains structures and substrate-bound SF1 and SF2 helicase structures, structure-function relationship, overview | Bacillus subtilis |
| physiological function | aromatic-rich loops as coupling motifs that link DNA binding and ATP hydrolysis, the conserved SF1 and SF2 helicase motifs mediate ATP binding and hydrolysis and convert the released chemical energy into the mechanical energy required for translocation and DNA unwinding | Escherichia coli |
| physiological function | aromatic-rich loops as coupling motifs that link DNA binding and ATP hydrolysis, the conserved SF1 and SF2 helicase motifs mediate ATP binding and hydrolysis and convert the released chemical energy into the mechanical energy required for translocation and DNA unwinding | Homo sapiens |
| physiological function | aromatic-rich loops as coupling motifs that link DNA binding and ATP hydrolysis, the conserved SF1 and SF2 helicase motifs mediate ATP binding and hydrolysis and convert the released chemical energy into the mechanical energy required for translocation and DNA unwinding | Geobacillus stearothermophilus |
| physiological function | aromatic-rich loops as coupling motifs that link DNA binding and ATP hydrolysis, the conserved SF1 and SF2 helicase motifs mediate ATP binding and hydrolysis and convert the released chemical energy into the mechanical energy required for translocation and DNA unwinding | Archaeoglobus fulgidus |
| physiological function | aromatic-rich loops as coupling motifs that link DNA binding and ATP hydrolysis, the conserved SF1 and SF2 helicase motifs mediate ATP binding and hydrolysis and convert the released chemical energy into the mechanical energy required for translocation and DNA unwinding | Bacillus subtilis |
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