https://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&feed=atom&action=historyGeneral Information/IS Organization - Revision history2024-03-29T10:47:19ZRevision history for this page on the wikiMediaWiki 1.34.0https://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=3050&oldid=prevTnCentral at 12:50, 5 December 20222022-12-05T12:50:14Z<p></p>
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</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=2989&oldid=prevTnCentral at 13:48, 4 December 20222022-12-04T13:48:35Z<p></p>
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</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=2704&oldid=prevTnCentral at 14:04, 21 March 20222022-03-21T14:04:23Z<p></p>
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</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=2188&oldid=prevTnCentral at 20:14, 9 August 20212021-08-09T20:14:34Z<p></p>
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<a href="https://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=1312&oldid=1118">Show changes</a>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=1118&oldid=prevTnCentral: /* Domain structure of transposases */2020-06-04T13:34:07Z<p><span dir="auto"><span class="autocomment">Domain structure of transposases</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Domain structure of transposases==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Domain structure of transposases==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Image:1.27.1.png|thumb|510x510px|'''Fig 1.27.1.''' Domain <del class="diffchange diffchange-inline">organisation </del>of transposases of the DDE family. The relative positions of the potential ZF, HTH, LZ and the ‘DDEK/R’ catalytic motif are indicated from left to right as light blue boxes. The figure illustrates the N-terminal and C-terminal extension of the different transposase examples. (a) Classical IS1 with frameshift. The position of the frameshift window which is used to generate InsAB is indicated. (b) IS1 without frameshift and the <del class="diffchange diffchange-inline">ISMhu11 </del>group showing the deletion of the ZF, the C-terminal extension, and the increased spacing between the second (d) and (e) residues. (c) The IS1595 family showing the classical <del class="diffchange diffchange-inline">IS1595 </del>group and the <del class="diffchange diffchange-inline">IS1016 </del>group which does not carry the N-terminal ZF. (d) The IS3 family including members with and without the translational frameshift. (e) The closely related IS481 family which lack the N-terminal HTH domain and exhibit an additional C-terminal domain.|alt=|left]]A general pattern for the functional organisation of Tpases appears to be emerging from the increasing number which have been analysed. Many can be divided into topologically distinct structural domains and, although several regions of the protein may contribute to a given function, the isolated domains themselves often exhibit a distinct function. The sequence-specific DNA binding activities of the proteins are generally located in the N-terminal region while the catalytic domain is often localised towards the C-terminal end: IS''1''<ref><nowiki><pubmed>2553980</pubmed></nowiki></ref><ref><nowiki><pubmed>2162466</pubmed></nowiki></ref>; IS''30''<ref><nowiki><pubmed>2154486</pubmed></nowiki></ref>;Mu, (see <ref><nowiki><pubmed>8556870</pubmed></nowiki></ref><ref><nowiki><pubmed>8646783</pubmed></nowiki></ref>; Tn''3''<ref><nowiki><pubmed>8382339</pubmed></nowiki></ref><ref><nowiki><pubmed>8080658</pubmed></nowiki></ref>; IS''50''<ref><nowiki><pubmed>8289277</pubmed></nowiki></ref>; IS''903''<ref><nowiki><pubmed>9417930</pubmed></nowiki></ref>; IS''911''<ref><nowiki><pubmed>8950268</pubmed></nowiki></ref>; for a review see <ref><nowiki><pubmed>10547692</pubmed></nowiki></ref> [[:Image:1.27.1.png|(Fig.1.27.1)]]. One functional interpretation of this arrangement for prokaryotic elements is that it may permit interaction of a nascent protein molecule with its target sequences on the IS thus coupling expression and activity. This notion is reinforced by the observation that the presence of the C-terminal region of the IS''50'', IS''10'' and IS''911'' Tpases appears to mask the DNA binding domain and reduce binding activity<ref><nowiki><pubmed>8057357</pubmed></nowiki></ref><ref><nowiki><pubmed>8412678</pubmed></nowiki></ref> possibly by masking the DNA binding domain. This arrangement might favor activity of the protein in cis, a property shared by several Tpases (see [[General Information/Transposase expression and activity#Co-translational binding and multimerization|Activity in cis]]). Similar masking appears to occur with the IS''1'' (D. Zerbib and M. Chandler, unpublished) and the IS''911''<ref><nowiki><pubmed>9761671</pubmed></nowiki></ref><ref><nowiki><pubmed>11352577</pubmed></nowiki></ref> Tpases. In several cases these domains are assembled into a single protein from consecutive orfs by translational frameshifting (Programmed translational frameshifting). In the case of IS''911'', it has been demonstrated that transposase binding to the IS ends occurs as the protein is translated<ref><nowiki><pubmed>22195971</pubmed></nowiki></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Image:1.27.1.png|thumb|510x510px|'''Fig 1.27.1.''' Domain <ins class="diffchange diffchange-inline">organization </ins>of transposases of the DDE family. The relative positions of the potential ZF, <ins class="diffchange diffchange-inline">[[wikipedia:Helix-turn-helix|</ins>HTH<ins class="diffchange diffchange-inline">]]</ins>, LZ<ins class="diffchange diffchange-inline">, </ins>and the ‘DDEK/R’ catalytic motif are indicated from left to right as light blue boxes. The figure illustrates the N-terminal and C-terminal extension of the different transposase examples. <ins class="diffchange diffchange-inline">'''</ins>(a)<ins class="diffchange diffchange-inline">''' </ins>Classical <ins class="diffchange diffchange-inline">[[IS Families/</ins>IS1 <ins class="diffchange diffchange-inline">family|IS''1'']] </ins>with frameshift. The position of the frameshift window which is used to generate <ins class="diffchange diffchange-inline">''</ins>InsAB<ins class="diffchange diffchange-inline">'' </ins>is indicated. <ins class="diffchange diffchange-inline">'''</ins>(b)<ins class="diffchange diffchange-inline">''' [[IS Families/</ins>IS1 <ins class="diffchange diffchange-inline">family|IS''1'']] </ins>without frameshift and the <ins class="diffchange diffchange-inline">IS''Mhu11'' </ins>group showing the deletion of the ZF, the C-terminal extension, and the increased spacing between the second <ins class="diffchange diffchange-inline">'''</ins>(d)<ins class="diffchange diffchange-inline">''' </ins>and <ins class="diffchange diffchange-inline">'''</ins>(e)<ins class="diffchange diffchange-inline">''' </ins>residues. <ins class="diffchange diffchange-inline">'''</ins>(c)<ins class="diffchange diffchange-inline">''' </ins>The <ins class="diffchange diffchange-inline">[[IS Families/</ins>IS1595 family<ins class="diffchange diffchange-inline">|IS''1595'' family]] </ins>showing the classical <ins class="diffchange diffchange-inline">IS''1595'' </ins>group and the <ins class="diffchange diffchange-inline">IS''1016'' </ins>group which does not carry the N-terminal ZF. <ins class="diffchange diffchange-inline">'''</ins>(d)<ins class="diffchange diffchange-inline">''' </ins>The <ins class="diffchange diffchange-inline">[[IS Families/</ins>IS3 family<ins class="diffchange diffchange-inline">|IS''3'' family]] </ins>including members with and without the translational frameshift. <ins class="diffchange diffchange-inline">'''</ins>(e)<ins class="diffchange diffchange-inline">''' </ins>The closely related <ins class="diffchange diffchange-inline">[[IS Families/</ins>IS481 family<ins class="diffchange diffchange-inline">|IS''481'' family]] </ins>which lack the N-terminal <ins class="diffchange diffchange-inline">[[wikipedia:Helix-turn-helix|</ins>HTH domain<ins class="diffchange diffchange-inline">]] </ins>and exhibit an additional C-terminal domain.|alt=|left]]A general pattern for the functional organisation of Tpases appears to be emerging from the increasing number which have been analysed. Many can be divided into topologically distinct structural domains and, although several regions of the protein may contribute to a given function, the isolated domains themselves often exhibit a distinct function. The sequence-specific DNA binding activities of the proteins are generally located in the N-terminal region while the catalytic domain is often localised towards the C-terminal end: IS''1''<ref><nowiki><pubmed>2553980</pubmed></nowiki></ref><ref><nowiki><pubmed>2162466</pubmed></nowiki></ref>; IS''30''<ref><nowiki><pubmed>2154486</pubmed></nowiki></ref>;Mu, (see <ref><nowiki><pubmed>8556870</pubmed></nowiki></ref><ref><nowiki><pubmed>8646783</pubmed></nowiki></ref>; Tn''3''<ref><nowiki><pubmed>8382339</pubmed></nowiki></ref><ref><nowiki><pubmed>8080658</pubmed></nowiki></ref>; IS''50''<ref><nowiki><pubmed>8289277</pubmed></nowiki></ref>; IS''903''<ref><nowiki><pubmed>9417930</pubmed></nowiki></ref>; IS''911''<ref><nowiki><pubmed>8950268</pubmed></nowiki></ref>; for a review see <ref><nowiki><pubmed>10547692</pubmed></nowiki></ref> [[:Image:1.27.1.png|(Fig.1.27.1)]]. One functional interpretation of this arrangement for prokaryotic elements is that it may permit interaction of a nascent protein molecule with its target sequences on the IS thus coupling expression and activity. This notion is reinforced by the observation that the presence of the C-terminal region of the IS''50'', IS''10'' and IS''911'' Tpases appears to mask the DNA binding domain and reduce binding activity<ref><nowiki><pubmed>8057357</pubmed></nowiki></ref><ref><nowiki><pubmed>8412678</pubmed></nowiki></ref> possibly by masking the DNA binding domain. This arrangement might favor activity of the protein in cis, a property shared by several Tpases (see [[General Information/Transposase expression and activity#Co-translational binding and multimerization|Activity in cis]]). Similar masking appears to occur with the IS''1'' (D. Zerbib and <ins class="diffchange diffchange-inline">[https://scholar.google.com/citations?user=r8TYgVEAAAAJ&hl=pt-BR </ins>M. Chandler<ins class="diffchange diffchange-inline">]</ins>, unpublished) and the IS''911''<ref><nowiki><pubmed>9761671</pubmed></nowiki></ref><ref><nowiki><pubmed>11352577</pubmed></nowiki></ref> Tpases. In several cases these domains are assembled into a single protein from consecutive orfs by translational frameshifting (Programmed translational frameshifting). In the case of IS''911'', it has been demonstrated that transposase binding to the IS ends occurs as the protein is translated<ref><nowiki><pubmed>22195971</pubmed></nowiki></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>One exception to this is the transposase of the [[IS Families/IS110 family|IS''110'' family]] which encodes a DEDD transposase closely related to the [[wikipedia:RuvABC|RuvC Holiday resolvase]] (see <ref><nowiki><pubmed>15866929</pubmed></nowiki></ref><ref><nowiki><pubmed>12897009</pubmed></nowiki></ref>) and in which the catalytic domain appears to precede the DNA binding domain.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>One exception to this is the transposase of the [[IS Families/IS110 family|IS''110'' family]] which encodes a DEDD transposase closely related to the [[wikipedia:RuvABC|RuvC Holiday resolvase]] (see <ref><nowiki><pubmed>15866929</pubmed></nowiki></ref><ref><nowiki><pubmed>12897009</pubmed></nowiki></ref>) and in which the catalytic domain appears to precede the DNA binding domain.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In addition to functional domains for DNA binding and catalysis, many, if not all transposases have the capacity to generate multimeric forms essential for their activity (see <ref><nowiki><pubmed>10547692</pubmed></nowiki></ref><ref><nowiki><pubmed>10677279</pubmed></nowiki></ref>). This is true of prokaryotic elements such as bacteriophage Mu (see <ref><nowiki><pubmed>8805293</pubmed></nowiki></ref>), IS''50''<ref><nowiki><pubmed>7958902</pubmed></nowiki></ref>, IS''911''<ref><nowiki><pubmed>9761671</pubmed></nowiki></ref><ref><nowiki><pubmed>11352577</pubmed></nowiki></ref><ref><nowiki><pubmed>10677279</pubmed></nowiki></ref>, IS''608'' and IS''Dra2''<ref><nowiki><pubmed>16209952</pubmed></nowiki></ref><ref><nowiki><pubmed>20890269</pubmed></nowiki></ref> (but apparently not IS''10''<ref><nowiki><pubmed>8565068</pubmed></nowiki></ref>, and of eukaryotic elements such as the retroviruses (see <ref><nowiki><pubmed>7526778</pubmed></nowiki></ref><ref><nowiki><pubmed>1322888</pubmed></nowiki></ref><ref><nowiki><pubmed>12446721</pubmed></nowiki></ref><ref><nowiki><pubmed>15718297</pubmed></nowiki></ref>) whose integrase (IN) (transposase) appears to be a dimer of dimers both with and without DNA bound<ref><nowiki><pubmed>12446721</pubmed></nowiki></ref><ref><nowiki><pubmed>17157316</pubmed></nowiki></ref><ref><nowiki><pubmed>19609359</pubmed></nowiki></ref><ref><nowiki><pubmed>19229293</pubmed></nowiki></ref> as does the purified P element transposase<ref><nowiki><pubmed>17644523</pubmed></nowiki></ref>, the mariner-like element, Mos1<ref><nowiki><pubmed>8913752</pubmed></nowiki></ref><ref><nowiki><pubmed>17565190</pubmed></nowiki></ref><ref><nowiki><pubmed>19766564</pubmed></nowiki></ref> and hermes (which appears to be an octomer)<ref><nowiki><pubmed>16041385</pubmed></nowiki></ref><ref><nowiki><pubmed>16511103</pubmed></nowiki></ref><ref><nowiki><pubmed>25036632</pubmed></nowiki></ref>. With the results of an increasing number of structural studies of these types of enzyme, it will be of great interest to compare the overall similarities of equivalent functional domains as has been recently possible with the catalytic domains of retroviral integrases, Mu transposase and other polynucleotidyl transferases such as the Holiday resolvase, RuvC and RnaseH (see <ref><nowiki><pubmed>8696976</pubmed></nowiki></ref><ref><nowiki><pubmed>8548793</pubmed></nowiki></ref>). One particular type of structure, a leucine zipper, clearly plays a vital role in multimerization of a number of transposases<ref><nowiki><pubmed>9761671</pubmed></nowiki></ref><ref><nowiki><pubmed>10677279</pubmed></nowiki></ref><ref><nowiki><pubmed>2147779</pubmed></nowiki></ref><ref><nowiki><pubmed>8647395</pubmed></nowiki></ref><ref><nowiki><pubmed>22032517</pubmed></nowiki></ref><ref><nowiki><pubmed>8643520</pubmed></nowiki></ref><ref><nowiki><pubmed>19416360</pubmed></nowiki></ref><ref><nowiki><pubmed>8520113</pubmed></nowiki></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In addition to functional domains for DNA binding and catalysis, many, if not all transposases have the capacity to generate multimeric forms essential for their activity (see <ref><nowiki><pubmed>10547692</pubmed></nowiki></ref><ref><nowiki><pubmed>10677279</pubmed></nowiki></ref>). This is true of prokaryotic elements such as bacteriophage Mu (see <ref><nowiki><pubmed>8805293</pubmed></nowiki></ref>), IS''50''<ref><nowiki><pubmed>7958902</pubmed></nowiki></ref>, IS''911''<ref><nowiki><pubmed>9761671</pubmed></nowiki></ref><ref><nowiki><pubmed>11352577</pubmed></nowiki></ref><ref><nowiki><pubmed>10677279</pubmed></nowiki></ref>, IS''608'' and IS''Dra2''<ref><nowiki><pubmed>16209952</pubmed></nowiki></ref><ref><nowiki><pubmed>20890269</pubmed></nowiki></ref> (but apparently not IS''10''<ref><nowiki><pubmed>8565068</pubmed></nowiki></ref>, and of eukaryotic elements such as the retroviruses (see <ref><nowiki><pubmed>7526778</pubmed></nowiki></ref><ref><nowiki><pubmed>1322888</pubmed></nowiki></ref><ref><nowiki><pubmed>12446721</pubmed></nowiki></ref><ref><nowiki><pubmed>15718297</pubmed></nowiki></ref>) whose integrase (IN) (transposase) appears to be a dimer of dimers both with and without DNA bound<ref><nowiki><pubmed>12446721</pubmed></nowiki></ref><ref><nowiki><pubmed>17157316</pubmed></nowiki></ref><ref><nowiki><pubmed>19609359</pubmed></nowiki></ref><ref><nowiki><pubmed>19229293</pubmed></nowiki></ref> as does the purified P element transposase<ref><nowiki><pubmed>17644523</pubmed></nowiki></ref>, the mariner-like element, Mos1<ref><nowiki><pubmed>8913752</pubmed></nowiki></ref><ref><nowiki><pubmed>17565190</pubmed></nowiki></ref><ref><nowiki><pubmed>19766564</pubmed></nowiki></ref> and hermes (which appears to be an octomer)<ref><nowiki><pubmed>16041385</pubmed></nowiki></ref><ref><nowiki><pubmed>16511103</pubmed></nowiki></ref><ref><nowiki><pubmed>25036632</pubmed></nowiki></ref>. With the results of an increasing number of structural studies of these types of enzyme, it will be of great interest to compare the overall similarities of equivalent functional domains as has been recently possible with the catalytic domains of retroviral integrases, Mu transposase and other polynucleotidyl transferases such as the Holiday resolvase, <ins class="diffchange diffchange-inline">[[wikipedia:RuvABC|</ins>RuvC<ins class="diffchange diffchange-inline">]] </ins>and <ins class="diffchange diffchange-inline">[[wikipedia:Ribonuclease_H|</ins>RnaseH<ins class="diffchange diffchange-inline">]] </ins>(see <ref><nowiki><pubmed>8696976</pubmed></nowiki></ref><ref><nowiki><pubmed>8548793</pubmed></nowiki></ref>). One particular type of structure, a leucine zipper, clearly plays a vital role in multimerization of a number of transposases<ref><nowiki><pubmed>9761671</pubmed></nowiki></ref><ref><nowiki><pubmed>10677279</pubmed></nowiki></ref><ref><nowiki><pubmed>2147779</pubmed></nowiki></ref><ref><nowiki><pubmed>8647395</pubmed></nowiki></ref><ref><nowiki><pubmed>22032517</pubmed></nowiki></ref><ref><nowiki><pubmed>8643520</pubmed></nowiki></ref><ref><nowiki><pubmed>19416360</pubmed></nowiki></ref><ref><nowiki><pubmed>8520113</pubmed></nowiki></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Finally, several DDE transposases exhibit what may be thought of as an “orphan” domain located between the second D and final E of the DDE motif<ref><nowiki><pubmed>23217365</pubmed></nowiki></ref> ([[General Information/Major Groups are Defined by the Type of Transposase They Use#Transposases examined by secondary structure prediction programs|Table transposases examined by secondary structure prediction programs]]). These can be either largely α-helical or β-stranded. It is likely that these insertion domains play subtle roles in the chemical pathways involved in the transposition of their cognate transposable elements. The largely β-stranded IS''50'' (Tn''5'') associated insertion domain ([[General Information/Major Groups are Defined by the Type of Transposase They Use#Major DDE transposition pathways|Major DDE transposition pathways]] - [[:Image:1.8.3.png|Fig.1.8.3)]]) interacts with and assists in stabilising a hairpin-loop structure at the transposon end formed as an intermediate during transposition<ref><nowiki><pubmed>10884228</pubmed></nowiki></ref><ref><nowiki><pubmed>15102449</pubmed></nowiki></ref><ref><nowiki><pubmed>17176076</pubmed></nowiki></ref> and therefore performs a crucial function. Another type of insertion domain is present at the same topological position in the eukaryotic Hermes transposase<ref><nowiki><pubmed>16041385</pubmed></nowiki></ref>. This long insertion domain is entirely α-helical. In contrast to Tn''5'' whose hairpin intermediate is formed on the transposon end, Hermes transposes using an intermediate in which a hairpin is formed on the flanking donor DNA<ref><nowiki><pubmed>15616554</pubmed></nowiki></ref><ref><nowiki><pubmed>30239795</pubmed></nowiki></ref>. It appears that the insertion domain assists stabilisation of the Hermes hairpin intermediate. A similar α-helical insertion has been identified in the VDJ recombinase, RAG1<ref><nowiki><pubmed>15616554</pubmed></nowiki></ref> which also generates a hairpin intermediate similar to that of Hermes. In Hermes, the domain also assists in forming transposase multimers.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Finally, several DDE transposases exhibit what may be thought of as an “orphan” domain located between the second D and final E of the DDE motif<ref><nowiki><pubmed>23217365</pubmed></nowiki></ref> ([[General Information/Major Groups are Defined by the Type of Transposase They Use#Transposases examined by secondary structure prediction programs|Table transposases examined by secondary structure prediction programs]]). These can be either largely α-helical or β-stranded. It is likely that these insertion domains play subtle roles in the chemical pathways involved in the transposition of their cognate transposable elements. The largely β-stranded IS''50'' (Tn''5'') associated insertion domain ([[General Information/Major Groups are Defined by the Type of Transposase They Use#Major DDE transposition pathways|Major DDE transposition pathways]] - [[:Image:1.8.3.png|Fig.1.8.3)]]) interacts with and assists in stabilising a hairpin-loop structure at the transposon end formed as an intermediate during transposition<ref><nowiki><pubmed>10884228</pubmed></nowiki></ref><ref><nowiki><pubmed>15102449</pubmed></nowiki></ref><ref><nowiki><pubmed>17176076</pubmed></nowiki></ref> and therefore performs a crucial function. Another type of insertion domain is present at the same topological position in the eukaryotic Hermes transposase<ref><nowiki><pubmed>16041385</pubmed></nowiki></ref>. This long insertion domain is entirely α-helical. In contrast to Tn''5'' whose hairpin intermediate is formed on the transposon end, Hermes transposes using an intermediate in which a hairpin is formed on the flanking donor DNA<ref><nowiki><pubmed>15616554</pubmed></nowiki></ref><ref><nowiki><pubmed>30239795</pubmed></nowiki></ref>. It appears that the insertion domain assists stabilisation of the Hermes hairpin intermediate. A similar α-helical insertion has been identified in the VDJ recombinase, RAG1<ref><nowiki><pubmed>15616554</pubmed></nowiki></ref> which also generates a hairpin intermediate similar to that of Hermes. In Hermes, the domain also assists in forming transposase multimers.</div></td></tr>
</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=1100&oldid=prevTnCentral at 18:42, 3 June 20202020-06-03T18:42:28Z<p></p>
<a href="https://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=1100&oldid=1099">Show changes</a>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=General_Information/IS_Organization&diff=1099&oldid=prevTnCentral at 18:38, 3 June 20202020-06-03T18:38:51Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:38, 3 June 2020</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">==General==</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<big>I</big>'''n addition to being small, insertion sequences are genetically compact [[:Image:1.25.1.png|(Fig.1.25.1)]]. They generally encode no functions other than those involved in their mobility although individual members of several families which include additional genes are now being identified. IS-encoded functions include factors required in cis, in particular recombinationally active DNA sequences that define the ends of the element together with an enzyme, the transposase (Tpase), which recognises and processes these ends. The Tpase is generally encoded by a single or perhaps two, open reading frames and consumes nearly the entire length of the element. [[Image:1.25.1.png|thumb|420x420px|'''Fig 1.25.1.''' General organization of IS ends.General organization of classical IS elements. The green box represents the IS element. Terminal inverted repeats (IRL and IRR) are shown in red. A single open reading frame (yellow) is shown within the IS. It stretches the entire length of the element and, although not always the case, is shown here to terminate within IRR. The indigenous Tpase promoter is located (by convention) in IRL. Transcription is from left to right. The arrows show that the protein acts on the ends of the element. The domain structure of the IRs is indicated by A (the region recognized by Tpase that is involved in cleavage) and B (the region to which Tpase binds in a sequence-specific way). XXX represents the short direct target repeat sequence that is duplicated during the insertion event.|alt=|border|center]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<big>I</big>'''n addition to being small, insertion sequences are genetically compact [[:Image:1.25.1.png|(Fig.1.25.1)]]. They generally encode no functions other than those involved in their mobility although individual members of several families which include additional genes are now being identified. IS-encoded functions include factors required in cis, in particular recombinationally active DNA sequences that define the ends of the element together with an enzyme, the transposase (Tpase), which recognises and processes these ends. The Tpase is generally encoded by a single or perhaps two, open reading frames and consumes nearly the entire length of the element. [[Image:1.25.1.png|thumb|420x420px|'''Fig 1.25.1.''' General organization of IS ends.General organization of classical IS elements. The green box represents the IS element. Terminal inverted repeats (IRL and IRR) are shown in red. A single open reading frame (yellow) is shown within the IS. It stretches the entire length of the element and, although not always the case, is shown here to terminate within IRR. The indigenous Tpase promoter is located (by convention) in IRL. Transcription is from left to right. The arrows show that the protein acts on the ends of the element. The domain structure of the IRs is indicated by A (the region recognized by Tpase that is involved in cleavage) and B (the region to which Tpase binds in a sequence-specific way). XXX represents the short direct target repeat sequence that is duplicated during the insertion event.|alt=|border|center]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Terminal inverted repeats==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Terminal inverted repeats==</div></td></tr>
</table>TnCentral