This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

Replication Termination Protein

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 10:19, 9 May 2017

Assymetric RTP dimer bound to the B site in a Ter region (PDB code 2dpd)

Drag the structure with the mouse to rotate

Diagram of RTP monomer with secondary structure highlighted.

1 Function
2 Termination of Replication
3 RTP Structure
4 Replication Mechanism

Function

The replication termination protein (RTP) is one of only two well-defined proteins known to be involved in arresting DNA replication forks, the other being a protein known as tus (termination utilisation substance) from E. coli ^[1]. RTP was discovered in Bacillus subtilis and has been identified as a DNA binding protein of the winged helix family that forms a dimer of 29kDa. This dimeric form has been shown to have an exceptionally high affinity for its cognate binding sites( Kd ~10-11M-1)^[2], otherwise known as Termination sites (Ter sites). These Ter sites are found in multiple locations in the B. subtilis genome ^[3]. For more details see:

Termination of Replication

B. subtilis genome showing origin of replication, polar Ter sites and both replication forks.

Bacterial replication like that found in Bacillus subtilis consists of two replication forks that travel in opposite directions around the same circular strand of DNA. These replication forks begin at the origin of replication (OriC) and travel in clockwise and anticlockwise directions ^[4]. To prevent the strand from being over replicated each strand needs to be terminated roughly opposite the OriC and then joined to form the complete duplicated strand of DNA. As such the Ter/RTP complexes have found to be polar in their action; that is that different Ter sites are capable of only blacking DNA replication from one direction only. Since Ter sites are found facing both forks of replication, and the combination of both are capable of stopping both strands of replication, they are often termed as replication traps. The arresting of replication is achieved by the binding of two dimers to each Ter site, with the two RTP binding sites referred to as site A and site B. Site B shows a higher affinity for RTP and binds first, with site A then being filled with another RTP dimer cooperatively. This differential affinity for RTP is cited as a possible reason for the observed polarity of the termination ^[5].

RTP Structure

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 end, first alpha helix , unstructured loop that is equivalent to the first beta sheet , helix loop helix structure (-), 2 beta sheets with a connecting loop that makes up the 'wing' structure and an additional long alpha helix involved in dimerisation .^[6]

Binding of Rtp to the assymetric B portion of the Ter site changes its conformation into an assymetric 'wing-up wing-down' structure.

The contacts upstream with rtp dimer bound to A-site while the : Contacts with phosphate backbone of downstream DNA

Residues that bind in both monomers: Red

Residues that bind only in wing-up: Green

Residues that bind only in wing-down: Blue

Both monomers	Unit	Binding
Lys14	Wing-down	Phosphate(13)
Gln15	Both	Phosphate(14)
Arg16	Both	Phosphate(13)
Tyr33	Wing-down	Phosphate(3)
Leu35	both	Phosphate(4)
Lys36	Wing-up	Sugar(3)
Asn53	Both	Phosphate(14)
His54	Both	Guanine(5)
Thr55	Both	Thymine(15)
Glu56	Wing-up	Phosphate(13)
Tyr58	Both	Phosphate(4/5)
Arg59	Both	Guanine(14)
His62	Both	Phosphate(5)
Gln72	Both	Phosphate(5)
Lys77	Wing-down	Phosphate(3)
Gln83	Wing-down	Sugar(3)
Val86	Wind-down	Phosphate(4)

^[7]

Replication Mechanism

Debate over the mechanism of Replication termination by RTP has led to a number of mechanisms being proposed. Original work on this question was hampered by an incorrect structure of RTP being released. This structure was produced in solution and was shown to be a symmetric dimer^[8] Later crystallisation of the protein bound to DNA showed the RTP formed a asymmetric dimer when bound to cognate sequences ^[9] . One early study proposed that the asymmetric interaction between terminator protein and terminator DNA contributed to the observed polarity, with later studies showing that the RTP/Ter complex contained partially unwound DNA, suggesting a locked complex was responsible. More recent data has implicated that protein -protein interactions between RTP and the helicase is primarily responsible for termination and that this mechanism is modulated by the asymmetrical interactions described above ^[10].

3D structures of replication terminator protein

1bm9 – BsRTP – Bacillus subtilis
1j0r, 2dqr - BsRTP (mutant)
2dpd - BsRTP + DNA
1f4k, 2dpu, 2efw – BsRTP (mutant) + DNA
1ecr – Tus + DNA – Escherichia coli

References

↑ Kamada K, Horiuchi T, Ohsumi K, Shimamoto N, Morkikawa K, (1996) Structure of a replication-terminator protein complexed with DNA. Nature, 383:598-603
↑ Wilce et. al. (2001) Structure of the RTP−DNA complex and the mechanism of polar replication fork arrest. Nature Structural Biology, 8:206-210
↑ Gautam A. et.al. (2001) A single domain of the replication termination protein of Bacillus subtilis is involved in arresting both DnaB helicase and RNA polymerase. Journal of Biological Chemistry, 276:23471-23479
↑ Noirot P (2007). "Replication of the Bacillus subtilis chromosome". In Graumann P. Bacillus: Cellular and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-12-7
↑ Duggin I.G. (2006) DNA Replication Fork Arrest by the Bacillus subtilis RTP–DNA Complex Involves a Mechanism that Is Independent of the Affinity of RTP–DNA Binding. Journal of Molecular Biology, 361:1-6
↑ Vivian JP, Porter CJ, Wilce JA, Wilce MCJ, (2007) An asymmetric structure of the Bacillus subtilise Replication Terminator Protein in Complex with DNA. J. Mol. Bio, 370:481-491
↑ Vivian JP, Porter CJ, Wilce JA, Wilce MCJ, (2007) An asymmetric structure of the Bacillus subtilise Replication Terminator Protein in Complex with DNA. J. Mol. Bio, 370:481-491
↑ Bastia D. (1995) Crystal structure of the replication terminator protein from b. subtilis at 2.6 A. Cell 80: 651-660
↑ Wilce et. al. (2001) Structure of the RTP−DNA complex and the mechanism of polar replication fork arrest. Nature Structural Biology, 8:206-210
↑ Kaplan D.L., Bastia D. (2009). Mechanisms of polar arrest of a replication fork. Molecular Microbiology 72: 279-284

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Craig Mooney, Joel L. Sussman

Retrieved from "http://52.214.119.220/wiki/index.php/Replication_Termination_Protein"

Category: Topic Page

@@ Line 25: / Line 25: @@
 ==RTP Structure==
-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>.<ref>Vivian JP, Porter CJ, Wilce JA, Wilce MCJ, (2007) An asymmetric structure of the Bacillus subtilise Replication Terminator Protein in Complex with DNA. J. Mol. Bio, 370:481-491</ref>
+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='44/449701/1/3'>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>.<ref>Vivian JP, Porter CJ, Wilce JA, Wilce MCJ, (2007) An asymmetric structure of the Bacillus subtilise Replication Terminator Protein in Complex with DNA. J. Mol. Bio, 370:481-491</ref>
 Binding of Rtp to the assymetric B portion of the Ter site changes its conformation into an assymetric 'wing-up wing-down' structure.

Replication Termination Protein

From Proteopedia

Revision as of 10:19, 9 May 2017

Contents

Function

Termination of Replication

RTP Structure

Replication Mechanism

3D structures of replication terminator protein

References

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox