Sandbox20: Difference between revisions

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===Structural Overview===

[[Image:RTP 1 Symmetry.jpg | thumb | upright=1.4| left| The two subunits of the RTP dimer complex.]]

[[Image:RTP 1 Symmetry.jpg | thumb | upright=1.4| left| The two subunits of the RTP dimer complex.]] [[Image:RTP Dimerisation.jpg | thumb | upright=1.2| right| Interactions between a4 helices facilitates dimerisation of RTP on the Ter DNA site.]] The structure of an RTP monomer bears greatest similarity to the "''classic winged-helix''" motif, where 'wings' project from the loop between the final two β sheets of a compact αβααββ structure. The two major variations from this theme are the absence of a β1 sheet (the corresponding region is termed the β1 loop), and the presence of a fourth elongate α-helix, which facilitates dimerisation. Each of these secondary structural elements are indicated in the structure <scene name='Sandbox20/2efw/8'>shown here</scene>.

The structure of an RTP monomer bears greatest similarity to the "''classic winged-helix''" motif, where 'wings' project from the loop between the final two β sheets of a compact αβααββ structure. The two major variations from this theme are the absence of a β1 sheet (the corresponding region is termed the β1 loop), and the presence of a fourth elongate α-helix, which facilitates dimerisation. Each of these secondary structural elements are indicated in the structure <scene name='Sandbox20/2efw/8'>shown here</scene>.

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[[Image:Tus 1 labelled helices.jpg | thumb | upright=1.6| left| Secondary structures of the Tus protein.]]

The structure of the Tus protein was determined in complex with TerA by Kamada et al., and shown to be a previously undescribed backbone conformation (<scene name='Sandbox20/Tus/2'>original image</scene>.). It is divided into two domains (amino and carboxy), in which α-helical regions of each are spanned by a central β-sandwich which contacts 13 bp of DNA duplex (#Indicate domains). ~~[[Image:RTP Dimerisation.jpg | thumb | upright=1.2| right| Interactions between a4 helices facilitates dimerisation of RTP on the Ter DNA site.]]~~ Three helices within the amino domain (αI αII, αIII) form an antiparallel bundle aligned parallel to the DNA (#Helix bundle). Another two helices (αIV, αV) clamp the DNA phosphate backbone at the non-permissive end, and forms the cytosine-specific pocket containing the crucial residues for anti-helicase activity (#Phosphate clamp). The main DNA-binding domain however is the exposed side of the double β sheet layer which provides several base-specific interactions. This lies within the major groove and causes a conformational change in the DNA involving a deepening of the major groove, and an expansion of the minor one (#Sheet position).

The structure of the Tus protein was determined in complex with TerA by Kamada et al., and shown to be a previously undescribed backbone conformation (<scene name='Sandbox20/Tus/2'>original image</scene>.). It is divided into two domains (amino and carboxy), in which α-helical regions of each are spanned by a central β-sandwich which contacts 13 bp of DNA duplex (#Indicate domains). Three helices within the amino domain (αI αII, αIII) form an antiparallel bundle aligned parallel to the DNA (#Helix bundle). Another two helices (αIV, αV) clamp the DNA phosphate backbone at the non-permissive end, and forms the cytosine-specific pocket containing the crucial residues for anti-helicase activity (#Phosphate clamp). The main DNA-binding domain however is the exposed side of the double β sheet layer which provides several base-specific interactions. This lies within the major groove and causes a conformational change in the DNA involving a deepening of the major groove, and an expansion of the minor one (#Sheet position).

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@@ Line 33: / Line 33: @@
 ===Structural Overview===
-[[Image:RTP 1 Symmetry.jpg | thumb | upright=1.4| left| The two subunits of the RTP dimer complex.]]
+[[Image:RTP 1 Symmetry.jpg | thumb | upright=1.4| left| The two subunits of the RTP dimer complex.]] [[Image:RTP Dimerisation.jpg | thumb | upright=1.2| right| Interactions between a4 helices facilitates dimerisation of RTP on the Ter DNA site.]] The structure of an RTP monomer bears greatest similarity to the "''classic winged-helix''" motif, where 'wings' project from the loop between the final two β sheets of a compact αβααββ structure. The two major variations from this theme are the absence of a β1 sheet (the corresponding region is termed the β1 loop), and the presence of a fourth elongate α-helix, which facilitates dimerisation. Each of these secondary structural elements are indicated in the structure <scene name='Sandbox20/2efw/8'>shown here</scene>.
-The structure of an RTP monomer bears greatest similarity to the "''classic winged-helix''" motif, where 'wings' project from the loop between the final two β sheets of a compact αβααββ structure. The two major variations from this theme are the absence of a β1 sheet (the corresponding region is termed the β1 loop), and the presence of a fourth elongate α-helix, which facilitates dimerisation. Each of these secondary structural elements are indicated in the structure <scene name='Sandbox20/2efw/8'>shown here</scene>.
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@@ Line 89: / Line 88: @@
 [[Image:Tus 1 labelled helices.jpg | thumb | upright=1.6| left| Secondary structures of the Tus protein.]]
-The structure of the Tus protein was determined in complex with TerA by Kamada et al., and shown to be a previously undescribed backbone conformation (<scene name='Sandbox20/Tus/2'>original image</scene>.). It is divided into two domains (amino and carboxy), in which α-helical regions of each are spanned by a central β-sandwich which contacts 13 bp of DNA duplex (#Indicate domains). [[Image:RTP Dimerisation.jpg | thumb | upright=1.2| right| Interactions between a4 helices facilitates dimerisation of RTP on the Ter DNA site.]] Three helices within the amino domain (αI αII, αIII) form an antiparallel bundle aligned parallel to the DNA (#Helix bundle). Another two helices (αIV, αV) clamp the DNA phosphate backbone at the non-permissive end, and forms the cytosine-specific pocket containing the crucial residues for anti-helicase activity (#Phosphate clamp). The main DNA-binding domain however is the exposed side of the double β sheet layer which provides several base-specific interactions. This lies within the major groove and causes a conformational change in the DNA involving a deepening of the major groove, and an expansion of the minor one (#Sheet position).
+The structure of the Tus protein was determined in complex with TerA by Kamada et al., and shown to be a previously undescribed backbone conformation (<scene name='Sandbox20/Tus/2'>original image</scene>.). It is divided into two domains (amino and carboxy), in which α-helical regions of each are spanned by a central β-sandwich which contacts 13 bp of DNA duplex (#Indicate domains). Three helices within the amino domain (αI αII, αIII) form an antiparallel bundle aligned parallel to the DNA (#Helix bundle). Another two helices (αIV, αV) clamp the DNA phosphate backbone at the non-permissive end, and forms the cytosine-specific pocket containing the crucial residues for anti-helicase activity (#Phosphate clamp). The main DNA-binding domain however is the exposed side of the double β sheet layer which provides several base-specific interactions. This lies within the major groove and causes a conformational change in the DNA involving a deepening of the major groove, and an expansion of the minor one (#Sheet position).
 space