Sandbox20: Difference between revisions
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<Structure load='2EFW' size='300' frame='true' align='right' caption='RTP' scene='Sandbox20/2efw/3' /> | <Structure load='2EFW' size='300' frame='true' align='right' caption='RTP' scene='Sandbox20/2efw/3' /> | ||
Two structurally identical RTP molecules form a dimeric complex upon binding to DNA. The Ter site is 30 bp in length, and contains an imperfect inverted 16 bp repeat overlapping at a highly conserved trinucleotide sequence (TAT). Differences in sequence distinguish the upstream ''Ter A'' domain from the downstream ''Ter B'' domain. These bind their respective RTP molecules in slightly different manners, creating an asymmetric complex which will only halt the progression of the replication fork if the B site is encountered first. The mechanism by which this is achieved is discussed below in relation to the structure of the <scene name='Sandbox20/2efw/3'>RTP complex</scene>. | Replication termination protein (RTP) binds to the Ter sites of B. subtilis, to halt progression of the replication fork. Two structurally identical RTP molecules form a dimeric complex upon binding to DNA. The Ter site is 30 bp in length, and contains an imperfect inverted 16 bp repeat overlapping at a highly conserved trinucleotide sequence (TAT). Differences in sequence distinguish the upstream ''Ter A'' domain from the downstream ''Ter B'' domain. These bind their respective RTP molecules in slightly different manners, creating an asymmetric complex which will only halt the progression of the replication fork if the B site is encountered first. The mechanism by which this is achieved is discussed below in relation to the structure of the <scene name='Sandbox20/2efw/3'>RTP complex</scene>. | ||
===Structural Overview=== | ===Structural Overview=== | ||
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The structure of an RTP monomer bears greatest similarity to the "''classic winged-helix''" motif, in which '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 instead 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, in which '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 instead 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 crystal structure of RTP was originally determined in 1995 <ref>PMID: 7867072</ref> in its unbound state, and submitted under the entry [[1bm9]]. Since then, three additional structures have been determined. The first of these, [[1F4K]], is of the RTP-DNA complex. The second, [[1J0R]] is of a single cysteine mutant. The most recent, [[2EFW]], indicates the DNA-RTP complex in its native state and reveals an insight into the molecular mechanism of contrahelicase activity. | |||
===DNA Binding=== | ===DNA Binding=== | ||
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The consequence of these different conformations is most prominent in the position of the B1 sheet. This is evident in the Tyr33 residue, <scene name='Sandbox20/2efw/20'>shown by clicking here</scene> | The consequence of these different conformations is most prominent in the position of the B1 sheet. This is evident in the Tyr33 residue, <scene name='Sandbox20/2efw/20'>shown by clicking here</scene> | ||
Space, which contact DNA only in the wing-down conformation. | Space, which contact DNA only in the wing-down conformation. | ||
==Tus== | ==Tus== | ||
