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Literature summary extracted from
- Thermostable DNA helicase improves the sensitivity of digital PCR (2018), Biochem. Biophys. Res. Commun., 495, 2189-2194 .
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 5.6.2.3 | gene TK_RS00875, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus (DE3) RIL | Thermococcus kodakarensis |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 5.6.2.3 | Mg2+ | required | Thermococcus kodakarensis |  |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.6.2.3 | ATP + H2O | Thermococcus kodakarensis | - |
ADP + phosphate | - |
? | |
| 5.6.2.3 | ATP + H2O | Thermococcus kodakarensis JCM 12380 | - |
ADP + phosphate | - |
? | |
| 5.6.2.3 | ATP + H2O | Thermococcus kodakarensis ATCC BAA-918 | - |
ADP + phosphate | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 5.6.2.3 | Thermococcus kodakarensis | Q5JFK3 | - |
- |
| 5.6.2.3 | Thermococcus kodakarensis ATCC BAA-918 | Q5JFK3 | - |
- |
| 5.6.2.3 | Thermococcus kodakarensis JCM 12380 | Q5JFK3 | - |
- |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.6.2.3 | ATP + H2O | - |
Thermococcus kodakarensis | ADP + phosphate | - |
? | |
| 5.6.2.3 | ATP + H2O | - |
Thermococcus kodakarensis JCM 12380 | ADP + phosphate | - |
? | |
| 5.6.2.3 | ATP + H2O | - |
Thermococcus kodakarensis ATCC BAA-918 | ADP + phosphate | - |
? | |
| 5.6.2.3 | additional information | the ATPase activity of Tk-Upf1 is determined using the single-stranded DNA (ssDNA) N-DNA70. When a 5' or 3' overhung mis-annealed primer is included as a competitive primer along with specific primers, noise DNAs derived from the misannealed primer are eliminated in the presence of Tk-Upf1. Among various double-stranded DNA (dsDNA) substrates (forked, 5' overhung, 3' overhung, and blunt-ended duplex), Tk-Upf1 has the highest unwinding activity toward 5' overhung DNAs. Noise DNAs are also eliminated in the presence of Tk-Upf1. Tk-Upf1 fully unwinds forked DNA, and has highest activity toward 5'-overhung DNA. Low activity with 3' overhung and blunt-ended duplex DNA, effect of Tk-Upf1 on PCR specificity. The enzyme unwinds mis-annealed primer/ template duplexes from the 5'-terminus during the annealing step of PCR, whereas primers perfectly bound to the target region are slightly peeled off by Tk-Upf1 | Thermococcus kodakarensis | ? | - |
- |
|
| 5.6.2.3 | additional information | the ATPase activity of Tk-Upf1 is determined using the single-stranded DNA (ssDNA) N-DNA70. When a 5' or 3' overhung mis-annealed primer is included as a competitive primer along with specific primers, noise DNAs derived from the misannealed primer are eliminated in the presence of Tk-Upf1. Among various double-stranded DNA (dsDNA) substrates (forked, 5' overhung, 3' overhung, and blunt-ended duplex), Tk-Upf1 has the highest unwinding activity toward 5' overhung DNAs. Noise DNAs are also eliminated in the presence of Tk-Upf1. Tk-Upf1 fully unwinds forked DNA, and has highest activity toward 5'-overhung DNA. Low activity with 3' overhung and blunt-ended duplex DNA, effect of Tk-Upf1 on PCR specificity. The enzyme unwinds mis-annealed primer/ template duplexes from the 5'-terminus during the annealing step of PCR, whereas primers perfectly bound to the target region are slightly peeled off by Tk-Upf1 | Thermococcus kodakarensis JCM 12380 | ? | - |
- |
|
| 5.6.2.3 | additional information | the ATPase activity of Tk-Upf1 is determined using the single-stranded DNA (ssDNA) N-DNA70. When a 5' or 3' overhung mis-annealed primer is included as a competitive primer along with specific primers, noise DNAs derived from the misannealed primer are eliminated in the presence of Tk-Upf1. Among various double-stranded DNA (dsDNA) substrates (forked, 5' overhung, 3' overhung, and blunt-ended duplex), Tk-Upf1 has the highest unwinding activity toward 5' overhung DNAs. Noise DNAs are also eliminated in the presence of Tk-Upf1. Tk-Upf1 fully unwinds forked DNA, and has highest activity toward 5'-overhung DNA. Low activity with 3' overhung and blunt-ended duplex DNA, effect of Tk-Upf1 on PCR specificity. The enzyme unwinds mis-annealed primer/ template duplexes from the 5'-terminus during the annealing step of PCR, whereas primers perfectly bound to the target region are slightly peeled off by Tk-Upf1 | Thermococcus kodakarensis ATCC BAA-918 | ? | - |
- |
|
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 5.6.2.3 | Tk-Upf1 | - |
Thermococcus kodakarensis |
| 5.6.2.3 | TK0178 | - |
Thermococcus kodakarensis |
| 5.6.2.3 | TK_RS00875 | - |
Thermococcus kodakarensis |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 5.6.2.3 | 100 | - |
recombinant enzyme | Thermococcus kodakarensis |
Temperature Range [°C]
| EC Number | Temperature Minimum [°C] | Temperature Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 5.6.2.3 | 70 | 100 | increasing activity within this range, inactive at 30-60°C | Thermococcus kodakarensis |
Temperature Stability [°C]
| EC Number | Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 5.6.2.3 | 60 | 90 | thermostability kinetics of purified recombinant enzyme, overview | Thermococcus kodakarensis |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 5.6.2.3 | 7.6 | - |
ATPase activity | Thermococcus kodakarensis |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 5.6.2.3 | evolution | DNA/RNA helicases are classified into six superfamilies (SF1e6) defined by a set of conserved sequence motifs. Tk-Upf1 is a superfamily 1B type helicase | Thermococcus kodakarensis |
| 5.6.2.3 | physiological function | fundamental properties of DNA/RNA helicases are nucleic acid binding, ATP hydrolysis, translocation, unwinding of duplex nucleic acids, and displacement of proteins bound to the nucleic acid substrate. Among various double-stranded DNA (dsDNA) substrates (forked, 5' overhung, 3' overhung, and blunt-ended duplex), Tk-Upf1 has the highest unwinding activity toward 5' overhung DNAs. Noise DNAs are also eliminated in the presence of Tk-Upf1 at concentrations 10fold lower than those required to yield a comparable reduction with Thermococcus kodakarensis superfamily 2B type helicase Tk-EshA | Thermococcus kodakarensis |
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