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Rtp and Tus DNA Binding: Difference between revisions

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==RTP==
==RTP==


RTP is a DNA binding protein from Bacillus Subtilis that uses a helix-loop-helix binding motif. In solution it shows a symmetric structure typical of the winged helix loop helix family, with an unstructured N-terminus end, first alpha helix (a1), unstructured loop that is equivalent to the first beta sheet (B1), helix loop helix structure (a2 - a3), 2 beta sheets with a connecting loop that makes up the 'wing' structure (B2 - B3) and an additional long alpha helix involved in dimerisation (a4).
RTP is a DNA binding protein from Bacillus Subtilis that uses a helix-loop-helix binding motif. In solution it shows a symmetric structure typical of the winged helix loop helix family, with an unstructured <scene name='Rtp_and_Tus_DNA_Binding/Nterm/1'>N-terminus</scene> end, first alpha helix <scene name='Rtp_and_Tus_DNA_Binding/Alpha1/1'>(a1)</scene>, unstructured loop that is equivalent to the first beta sheet <scene name='Rtp_and_Tus_DNA_Binding/Beta1/1'>(B1)</scene>, helix loop helix structure (<scene name='Rtp_and_Tus_DNA_Binding/Alpha2/1'>a2</scene>-<scene name='Rtp_and_Tus_DNA_Binding/Alpha3/1'>a3</scene>), 2 beta sheets with a connecting loop that makes up the 'wing' structure <scene name='Rtp_and_Tus_DNA_Binding/Wing/1'>(B2 - B3)</scene> and an additional long alpha helix involved in dimerisation <scene name='Rtp_and_Tus_DNA_Binding/Alpha4/1'>(a4)</scene>.


Assymmetry of RTP in DNA-binding


{{STRUCTURE_1bm9 |  PDB=1bm9  |  SCENE=  }}
<scene name='Rtp_and_Tus_DNA_Binding/Wingup/1'>Wing-up</scene>: Contacts upstream with rtp dimer bound to A-site


<scene name='Rtp_and_Tus_DNA_Binding/Wingdown/1'>Wing-down</scene>: Contacts with phosphate backbone of downstream DNA


==Binding to B site==


The RTP binding site consists of a 30bp sequence consisting of two inperfect 16 bp repeats, the A site and the B site.
Residues binding to DNA


<scene name ='overview'> click here </scene>
<Structure load='Lol1.pdb' size='400' caption= color='white'/>


<Structure load='Lol1.pdb' size='500' color='white'/>
==3D structures of replication termination protein==
 
[[Replication Termination Protein]]

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Craig Mooney, Michal Harel
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