Sandbox20: Difference between revisions

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==Tus==

===Role===

Tus is the 36 kDa protein responsible for termination of replication in Escherichia coli. The chromosome of E. coli contains a set of six polar Ter DNA sequences arranged such that three with the same directionality are located on either half of the chromosome. This generates what is termed a replication-fork trap, which prevents replication from occurring towards the origin. The Ter sites contain a 20 bp consensus element to which a monomer of Termination Utilisation Substance (Tus) binds to form a polar DNA-protein complex which halts the progression of the replicative machinery from one direction only. The fork arrest mechanism depends on the blocking of the helicase activity of DnaB, which is the first component of the replisome to encounter the Ter-Tus¬ complex.

===Structural Overview===

~~Original picture is~~ <scene name='Sandbox20/Tus/2'>~~shown by clicking here~~</scene>.

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).

===DNA Binding===

Tus ~~binds~~ by ~~an interaction~~ between beta sheets (shown in green) and the major groove of DNA~~. This is~~ <scene name='Sandbox20/Tus/19'>shown here</scene>.

Tus is among the most stable monomeric, sequence-specific, double-stranded DNA-binding proteins. Three major sets of interactions contribute to this; (1) the phosphate clamp within the amino domain, (2) base-specific polar interactions by the β-sheet within the major groove, and (3) non-polar contacts within the carboxy domain.

1. Interaction between beta sheets (shown in green) and the major groove of DNA (<scene name='Sandbox20/Tus/19'>shown here</scene>).

===Replication Termination Activity===

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@@ Line 54: / Line 54: @@
 ==Tus==
 <Structure load='2EWJ' size='300' frame='true' align='right' caption='Tus' scene='Sandbox20/Tus/2' />
+===Role===
+Tus is the 36 kDa protein responsible for termination of replication in Escherichia coli. The chromosome of E. coli contains a set of six polar Ter DNA sequences arranged such that three with the same directionality are located on either half of the chromosome. This generates what is termed a replication-fork trap, which prevents replication from occurring towards the origin. The Ter sites contain a 20 bp consensus element to which a monomer of Termination Utilisation Substance (Tus) binds to form a polar DNA-protein complex which halts the progression of the replicative machinery from one direction only. The fork arrest mechanism depends on the blocking of the helicase activity of DnaB, which is the first component of the replisome to encounter the Ter-Tus¬ complex.
 ===Structural Overview===
-Original picture is <scene name='Sandbox20/Tus/2'>shown by clicking here</scene>.
+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).
 ===DNA Binding===
-Tus binds by an interaction between beta sheets (shown in green) and the major groove of DNA. This is <scene name='Sandbox20/Tus/19'>shown here</scene>.
+Tus is among the most stable monomeric, sequence-specific, double-stranded DNA-binding proteins. Three major sets of interactions contribute to this; (1) the phosphate clamp within the amino domain, (2) base-specific polar interactions by the β-sheet within the major groove, and (3) non-polar contacts within the carboxy domain.
+. Interaction between beta sheets (shown in green) and the major groove of DNA (<scene name='Sandbox20/Tus/19'>shown here</scene>).
 ===Replication Termination Activity===