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Literature summary for 3.6.4.13 extracted from
- A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner (2018), Nucleic Acids Res., 46, 2648-2659 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| recombinant expression of wild-type and mutant isozymes, that are CBP-tagged at the N-terminus and His-tagged at the C-terminus, in Escherichia coli strain BL21(DE3) | Homo sapiens |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant helicase core of UPF1_1 in its apo-state, X-ray diffraction structure determination and analysis at 3.34 A resolution. Analysis of the X-ray crystal structures of the different states of UPF1_2DELTACH mutant | Homo sapiens |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | generation of the DELTAUPF1_1x02loop and UPF1_1DELTACHx02loop mutants, and of truncation mutant UPF1_2DELTACH | Homo sapiens |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| additional information | Comparison of the ATPase activities of UPF1_1 and UPF1_2 shows that a longer regulatory loop does not inhibit the catalytic activity of the helicase. In fact, UPF1_1 shows a marginally higher ATPase activity than UPF1_2. ATP-dependent helicase assays with UPF11 and UPF12 also show that the unwinding activity of UPF1 is not inhibited by a longer regulatory loop | Homo sapiens |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | stopped flow assays, kinetics analysis and comparison of wild-type and mutant Upf isozymes with ATP, overview | Homo sapiens |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | 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 | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Homo sapiens | Q92900 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant CBP- and His-tagged wild-type and mutant isozymes from Escherichia coli strain BL21(DE3) by nickel affinity and calmodulin affinity chromatography, followed by dialysis | Homo sapiens |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + H2O | - |
Homo sapiens | ADP + phosphate | - |
? | |
| additional information | the two isoforms of UPF differ in their RNA-binding and catalytic activities, the flexible loop in domain 1B affects the catalytic activity of UPF1 isozymes | Homo sapiens | ? | - |
- |
|
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| ATP-dependent helicase | - |
Homo sapiens |
| RENT1 | - |
Homo sapiens |
| RNA helicase UPF1 | - |
Homo sapiens |
| Upf1 | - |
Homo sapiens |
| UPF1_1 | - |
Homo sapiens |
| UPF1_2 | - |
Homo sapiens |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 30 | - |
assay at, ATPase assay | Homo sapiens |
| 37 | - |
assay at, helicase assay | Homo sapiens |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 6.5 | - |
assay at, ATPase assay | Homo sapiens |
| 7.5 | - |
assay at, helicase assay | Homo sapiens |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | UPF1 exists as two alternatively-spliced isoforms in mammals, which differ only in the length of this regulatory loop | Homo sapiens |
| metabolism | the RNA helicase UPF1 is a key component of the nonsense mediated mRNA decay (NMD) pathway | Homo sapiens |
| additional information | a conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner. UPF1 molecular mechanisms, catalytic activity and regulation, overview. The regulatory loop in isoform 1 (UPF1_1) is 11 residues longer than that of isoform 2 (UPF1_2). This small insertion in UPF11 leads to a 2fold increase in its translocation and ATPase activities. Structure analysis and comparisons of wild-type and mutant forms of the two isozymes, detailed overview | Homo sapiens |
| physiological function | analysis of a distinct mechanism of regulation of RNA helicases, wherein alternative splicing leads to subtle structural rearrangements within the protein that are critical to modulate enzyme movements and catalytic activity | Homo sapiens |
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