Transcription-repair coupling factor - Revision history

Michal Harel at 11:03, 31 December 2023

Michal Harel — Sun, 31 Dec 2023 11:03:33 GMT

←Older revision		Revision as of 11:03, 31 December 2023
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		+	__TOC__
	The bacterial [[transcription-repair coupling factor]] TRCF, also called Mfd translocase, is a DNA repair protein. It has a role in transcription-coupled repair, a subpathway of nucleotide excision repair (NER). Mfd recognizes stalled RNA polymerase (RNAP) and either restarts transcription or removes the stalled polymerase and recruits the NER proteins UvrA and UvrB.		The bacterial [[transcription-repair coupling factor]] TRCF, also called Mfd translocase, is a DNA repair protein. It has a role in transcription-coupled repair, a subpathway of nucleotide excision repair (NER). Mfd recognizes stalled RNA polymerase (RNAP) and either restarts transcription or removes the stalled polymerase and recruits the NER proteins UvrA and UvrB.

Michal Harel at 11:02, 31 December 2023

Michal Harel — Sun, 31 Dec 2023 11:02:51 GMT

←Older revision		Revision as of 11:02, 31 December 2023
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	== 3D Structures of Transcription-repair coupling factor ==		== 3D Structures of Transcription-repair coupling factor ==
	[[Transcription-repair coupling factor 3D structures]]		[[Transcription-repair coupling factor 3D structures]]
-
-	</StructureSection>

	== References ==		== References ==
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	[[Category:Topic Page]]		[[Category:Topic Page]]
	<br />		<br />
		+	</StructureSection>
	Created with the participation of [[User:Wayne Decatur\|Wayne Decatur]]		Created with the participation of [[User:Wayne Decatur\|Wayne Decatur]]

Michal Harel at 07:28, 1 May 2022

Michal Harel — Sun, 01 May 2022 07:28:03 GMT

←Older revision		Revision as of 07:28, 1 May 2022
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	In the apo-structure, domains 3 and 4 are far apart from each other (connected by an extended linker), but they make direct contacts when Mfd is loaded on DNA. On the other hand, domains 4 and 5 make direct contacts in the apo-structure, but are far apart from each other (coonected by an extended linker) when Mfd is loaded on DNA. Finally, domain 2 and domain 7 bind to each other in the apo-state whereas domain 2 is available for binding UvrA in the DNA-bound state.		In the apo-structure, domains 3 and 4 are far apart from each other (connected by an extended linker), but they make direct contacts when Mfd is loaded on DNA. On the other hand, domains 4 and 5 make direct contacts in the apo-structure, but are far apart from each other (coonected by an extended linker) when Mfd is loaded on DNA. Finally, domain 2 and domain 7 bind to each other in the apo-state whereas domain 2 is available for binding UvrA in the DNA-bound state.
		+
	== 3D Structures of Transcription-repair coupling factor ==		== 3D Structures of Transcription-repair coupling factor ==
	[[Transcription-repair coupling factor 3D structures]]		[[Transcription-repair coupling factor 3D structures]]
		+
	</StructureSection>		</StructureSection>

Michal Harel at 07:27, 1 May 2022

Michal Harel — Sun, 01 May 2022 07:27:04 GMT

←Older revision		Revision as of 07:27, 1 May 2022
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	== References ==		== References ==
	<references/>		<references/>
-
-	== 3D Structures of Transcription-repair coupling factor ==
-
-	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-
-	[[2eyq]] – EcTRCF – ''Escherichia coli''<br />
-	[[6x2n]], [[6x2f]], [[6x26]], [[6x50]], [[6x43]], [[6x4w]], [[6x4y]] - EcTRCF, RNA polymerase, RNA, DNA (Cryo EM)<br />
-	[[3hjh]] – EcTRCF residues 1-470<br />
-	[[2b2n]] - EcTRCF residues 1-333<br />
-	[[6yhz]] - EcTRCF residues 472-547 – NMR<br />
-	[[4dfc]] – EcTRCF D2 domain 127-213 + UvrABC system protein A<br />
-	[[6xeo]] – EcTRCF + DNA – Cryo EM<br />
-	[[6x26]] – EcTRCF in RNA polymerase complex – Cryo EM<br />
-	[[6x2f]], [[6x4w]], [[6x4y]] – EcTRCF in RNA polymerase complex + ADP – Cryo EM<br />
-	[[6x2n]], [[6x43]], [[6x50]] – EcTRCF in RNA polymerase complex + ATP – Cryo EM<br />
-	[[3mlq]] – TtTRCF RNA polymerase interacting domain + DNA-directed RNA polymerase subunit β - ''Thermus thermophilus''<br />
-	[[6m6a]] – TtTRCF in RNA polymerase complex – Cryo EM<br />
-	[[6m6b]] – TtTRCF in RNA polymerase complex + ATP-γ-S – Cryo EM<br />
-	[[2qsr]] – TRCF C terminal – ''Streptococcus pneumoni''<br />
-	[[6ac6]], [[6aca]], [[6ac8]] – MsTRCF – ''Mycobacterium smegmatis''<br />
-	[[6acx]] – MsTRCF + ADP<br />
-

	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

Michal Harel at 07:24, 1 May 2022

Michal Harel — Sun, 01 May 2022 07:24:44 GMT

←Older revision		Revision as of 07:24, 1 May 2022
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	In the apo-structure, domains 3 and 4 are far apart from each other (connected by an extended linker), but they make direct contacts when Mfd is loaded on DNA. On the other hand, domains 4 and 5 make direct contacts in the apo-structure, but are far apart from each other (coonected by an extended linker) when Mfd is loaded on DNA. Finally, domain 2 and domain 7 bind to each other in the apo-state whereas domain 2 is available for binding UvrA in the DNA-bound state.		In the apo-structure, domains 3 and 4 are far apart from each other (connected by an extended linker), but they make direct contacts when Mfd is loaded on DNA. On the other hand, domains 4 and 5 make direct contacts in the apo-structure, but are far apart from each other (coonected by an extended linker) when Mfd is loaded on DNA. Finally, domain 2 and domain 7 bind to each other in the apo-state whereas domain 2 is available for binding UvrA in the DNA-bound state.
-		+	== 3D Structures of Transcription-repair coupling factor ==
		+	[[Transcription-repair coupling factor 3D structures]]
	</StructureSection>		</StructureSection>

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	[[4dfc]] – EcTRCF D2 domain 127-213 + UvrABC system protein A<br />		[[4dfc]] – EcTRCF D2 domain 127-213 + UvrABC system protein A<br />
	[[6xeo]] – EcTRCF + DNA – Cryo EM<br />		[[6xeo]] – EcTRCF + DNA – Cryo EM<br />
		+	[[6x26]] – EcTRCF in RNA polymerase complex – Cryo EM<br />
		+	[[6x2f]], [[6x4w]], [[6x4y]] – EcTRCF in RNA polymerase complex + ADP – Cryo EM<br />
		+	[[6x2n]], [[6x43]], [[6x50]] – EcTRCF in RNA polymerase complex + ATP – Cryo EM<br />
	[[3mlq]] – TtTRCF RNA polymerase interacting domain + DNA-directed RNA polymerase subunit β - ''Thermus thermophilus''<br />		[[3mlq]] – TtTRCF RNA polymerase interacting domain + DNA-directed RNA polymerase subunit β - ''Thermus thermophilus''<br />
-	[[6m6a]] – TtTRCF + RNA polymerase – Cryo EM<br />	+	[[6m6a]] – TtTRCF in RNA polymerase complex – Cryo EM<br />
-	[[6m6b]] – TtTRCF + RNA polymerase + ATP-γ-S – Cryo EM<br />	+	[[6m6b]] – TtTRCF in RNA polymerase complex + ATP-γ-S – Cryo EM<br />
	[[2qsr]] – TRCF C terminal – ''Streptococcus pneumoni''<br />		[[2qsr]] – TRCF C terminal – ''Streptococcus pneumoni''<br />
	[[6ac6]], [[6aca]], [[6ac8]] – MsTRCF – ''Mycobacterium smegmatis''<br />		[[6ac6]], [[6aca]], [[6ac8]] – MsTRCF – ''Mycobacterium smegmatis''<br />

Karsten Theis: /* Structure and conformational change */

Karsten Theis — Mon, 16 Aug 2021 15:17:33 GMT

Structure and conformational change

←Older revision		Revision as of 15:17, 16 August 2021
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	== Structure and conformational change ==		== Structure and conformational change ==
	<StructureSection load='' size='350' side='right' scene='2eyq/Domainscolorsflabe/3' caption=''>		<StructureSection load='' size='350' side='right' scene='2eyq/Domainscolorsflabe/3' caption=''>
-	The initial scene (switch to <scene name='46/460252/Apo/1'>cartoon</scene>) shows the domains of Mfd in the conformation of the apo-enzyme.<ref>DOI:10.1016/j.cell.2005.11.045</ref> The UvrA interaction site (on domain 2) is occluded by domain 7. The translocase domains (domain 5 and domain 6), through interactions with domains 1 and 3, are locked in an inactive conformation, preventing the typical hinge motion of translocases when they bind and hydrolyze ATP while moving along DNA. When Mfd binds to DNA in the presence of ~~ADP AlFx~~, Mfd undergoes large domain rearrangements, giving a hint how it might bind to stalled RNAP.<ref>DOI:10.1038/s41467-020-17457-1</ref>. A first glimpse of the Mfd RNAP complex was through cryo-EM, but large parts of the Mfd protein were not resolved.<ref>DOI:10.1093/nar/gkaa904</ref>	+	The initial scene (switch to <scene name='46/460252/Apo/1'>cartoon</scene>) shows the domains of Mfd in the conformation of the apo-enzyme.<ref>DOI:10.1016/j.cell.2005.11.045</ref> The UvrA interaction site (on domain 2) is occluded by domain 7. The translocase domains (domain 5 and domain 6), through interactions with domains 1 and 3, are locked in an inactive conformation, preventing the typical hinge motion of translocases when they bind and hydrolyze ATP while moving along DNA. When Mfd binds to DNA in the presence of ADP·AlFₓ, Mfd undergoes large domain rearrangements, giving a hint how it might bind to stalled RNAP.<ref>DOI:10.1038/s41467-020-17457-1</ref> A first glimpse of the Mfd RNAP complex was through cryo-EM, but large parts of the Mfd protein were not resolved.<ref>DOI:10.1093/nar/gkaa904</ref>

	[[Image:Mfd domains.JPG\|thumb\|left]]		[[Image:Mfd domains.JPG\|thumb\|left]]

Karsten Theis: /* Structure and conformational change */

Karsten Theis — Mon, 16 Aug 2021 15:16:04 GMT

Structure and conformational change

←Older revision		Revision as of 15:16, 16 August 2021
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	[[Image:Mfd domains.JPG\|thumb\|left]]		[[Image:Mfd domains.JPG\|thumb\|left]]

-	In 2021, the structures of several intermediates in the presences of stalled RNAP were determined using cryo-EM, shedding light on the loading and activation mechanism, as well as how translocation of Mfd on DNA leads to disruption of the RNAP elongation complex and recruitment of UvrA.<ref>doi: 10.7554/eLife.62117</ref>	+	In 2021, the structures of several intermediates in the presences of stalled RNAP were determined using cryo-EM, shedding further light on the loading and activation mechanism, as well as how translocation of Mfd on DNA leads to disruption of the RNAP elongation complex and recruitment of UvrA.<ref>doi: 10.7554/eLife.62117</ref>
	When <scene name='46/460252/Mfd_rnap_l1/2'>Mfd binds to a stalled RNA polymerase</scene>, the RID (domain 4) binds to the beta subunit of RNA polymerase and domains 5 and domain 6 bind to DNA and ATP. These multiple binding events require a different relative orientation of RID and the translocase domains, and the necessary conformational changes disrupt inter-domain interactions seen in the apo-structure while activating the translocase activity of Mfd.		When <scene name='46/460252/Mfd_rnap_l1/2'>Mfd binds to a stalled RNA polymerase</scene>, the RID (domain 4) binds to the beta subunit of RNA polymerase and domains 5 and domain 6 bind to DNA and ATP. These multiple binding events require a different relative orientation of RID and the translocase domains, and the necessary conformational changes disrupt inter-domain interactions seen in the apo-structure while activating the translocase activity of Mfd.

Karsten Theis: /* Structure and conformational change */

Karsten Theis — Mon, 16 Aug 2021 14:42:36 GMT

Structure and conformational change

←Older revision		Revision as of 14:42, 16 August 2021
Line 9:		Line 9:
	== Structure and conformational change ==		== Structure and conformational change ==
	<StructureSection load='' size='350' side='right' scene='2eyq/Domainscolorsflabe/3' caption=''>		<StructureSection load='' size='350' side='right' scene='2eyq/Domainscolorsflabe/3' caption=''>
-	The initial scene (switch to <scene name='46/460252/Apo/1'>cartoon</scene>) shows the domains of Mfd in the conformation of the apo-enzyme.<ref>DOI:10.1016/j.cell.2005.11.045</ref> The UvrA interaction site (on domain 2) is occluded by domain 7. The translocase domains (domain 5 and domain 6), through interactions with domains 1 and 3, are locked in an inactive conformation, preventing the typical hinge motion of translocases when they bind and hydrolyze ATP while moving along DNA.	+	The initial scene (switch to <scene name='46/460252/Apo/1'>cartoon</scene>) shows the domains of Mfd in the conformation of the apo-enzyme.<ref>DOI:10.1016/j.cell.2005.11.045</ref> The UvrA interaction site (on domain 2) is occluded by domain 7. The translocase domains (domain 5 and domain 6), through interactions with domains 1 and 3, are locked in an inactive conformation, preventing the typical hinge motion of translocases when they bind and hydrolyze ATP while moving along DNA. When Mfd binds to DNA in the presence of ADP AlFx, Mfd undergoes large domain rearrangements, giving a hint how it might bind to stalled RNAP.<ref>DOI:10.1038/s41467-020-17457-1</ref>. A first glimpse of the Mfd RNAP complex was through cryo-EM, but large parts of the Mfd protein were not resolved.<ref>DOI:10.1093/nar/gkaa904</ref>

	[[Image:Mfd domains.JPG\|thumb\|left]]		[[Image:Mfd domains.JPG\|thumb\|left]]

-	When <scene name='46/460252/Mfd_rnap_l1/2'>Mfd binds to a stalled RNA polymerase</scene>, the RID (domain 4) binds to the beta subunit of RNA polymerase and domains 5 and domain 6 bind to DNA and ATP. These multiple binding events require a different relative orientation of RID and the translocase domains, and the necessary conformational changes disrupt inter-domain interactions seen in the apo-structure while activating the translocase activity of Mfd<ref>doi: 10.7554/eLife.62117</ref>. The structures of several intermediates in the presences of stalled RNAP were determined using cryo-EM, shedding light on the loading and activation mechanism, as well as how translocation of Mfd on DNA leads to disruption of the RNAP elongation complex and recruitment of UvrA.	+	In 2021, the structures of several intermediates in the presences of stalled RNAP were determined using cryo-EM, shedding light on the loading and activation mechanism, as well as how translocation of Mfd on DNA leads to disruption of the RNAP elongation complex and recruitment of UvrA.<ref>doi: 10.7554/eLife.62117</ref>
		+	When <scene name='46/460252/Mfd_rnap_l1/2'>Mfd binds to a stalled RNA polymerase</scene>, the RID (domain 4) binds to the beta subunit of RNA polymerase and domains 5 and domain 6 bind to DNA and ATP. These multiple binding events require a different relative orientation of RID and the translocase domains, and the necessary conformational changes disrupt inter-domain interactions seen in the apo-structure while activating the translocase activity of Mfd.

	Once the translocase domains are activated, they move closer and closer to the surface of the RNA polymerase in multiple cycles of ATP hydrolysis until <scene name='46/460252/Mfd_rnap_l2/2'>they make contact</scene>. The translocase moving along the DNA together with the RID tethered at a fixed point on the RNAP surface result in substantial reorganization of the domain contacts and relative orientation. Eventually, this leads to the the <scene name='46/460252/Mfd_rnap_c4/1'>UvrA interaction site on domain 2 (cyan) becoming available for UvrA</scene>, thus recruiting the NER machinery to the damaged template strand for subsequent repair. Further translocation (not shown) will lead to distabilization of the RNAP: nucleic acid complex, helping to dislodge the stalled RNAP. The changing domain contacts are schematically summarized below.		Once the translocase domains are activated, they move closer and closer to the surface of the RNA polymerase in multiple cycles of ATP hydrolysis until <scene name='46/460252/Mfd_rnap_l2/2'>they make contact</scene>. The translocase moving along the DNA together with the RID tethered at a fixed point on the RNAP surface result in substantial reorganization of the domain contacts and relative orientation. Eventually, this leads to the the <scene name='46/460252/Mfd_rnap_c4/1'>UvrA interaction site on domain 2 (cyan) becoming available for UvrA</scene>, thus recruiting the NER machinery to the damaged template strand for subsequent repair. Further translocation (not shown) will lead to distabilization of the RNAP: nucleic acid complex, helping to dislodge the stalled RNAP. The changing domain contacts are schematically summarized below.

Karsten Theis: /* Structure and conformational change */

Karsten Theis — Mon, 16 Aug 2021 14:26:20 GMT

Structure and conformational change

←Older revision		Revision as of 14:26, 16 August 2021
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	[[Image:Mfd domain contacts.JPG\|400px\|thumb\|center\|Distinct domain contacts in various Mfd structures]]		[[Image:Mfd domain contacts.JPG\|400px\|thumb\|center\|Distinct domain contacts in various Mfd structures]]

-	One of the functions of the large conformational change is to create a topological lock around the DNA to support translocation in a highly processive manner. Whereas in other ~~system~~, motor protein, clamp and clamp loader are separate proteins, all these functions are housed here in a single polypeptide. Mfd uses a single ATPase activity to create a sliding clamp and load it onto the DNA. The necessary reorganization of domains is visualized in a <scene name='46/460252/Mfd_domain_contacts/2'>morph</scene>. <ref>The [[Jmol/Storymorph\|Storymorph Jmol scripts]] were used to create the interpolation shown in the morph. [https://proteopedia.org/wiki/index.php/Image:Morph_mfd_contacts.pdb Coordinates] available on Proteopedia</ref>	+	One of the functions of the large conformational change is to create a topological lock around the DNA to support translocation in a highly processive manner. Whereas in other systems, motor protein, clamp and clamp loader are separate proteins, all these functions are housed here in a single polypeptide. Mfd uses a single ATPase activity to create a sliding clamp and load it onto the DNA. The necessary reorganization of domains is visualized in a <scene name='46/460252/Mfd_domain_contacts/2'>morph</scene>. <ref>The [[Jmol/Storymorph\|Storymorph Jmol scripts]] were used to create the interpolation shown in the morph. [https://proteopedia.org/wiki/index.php/Image:Morph_mfd_contacts.pdb Coordinates] available on Proteopedia</ref>
	{{Template:Button Toggle Animation2}}		{{Template:Button Toggle Animation2}}

Karsten Theis at 14:20, 16 August 2021

Karsten Theis — Mon, 16 Aug 2021 14:20:49 GMT

←Older revision		Revision as of 14:20, 16 August 2021
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	== Structure and conformational change ==		== Structure and conformational change ==
	<StructureSection load='' size='350' side='right' scene='2eyq/Domainscolorsflabe/3' caption=''>		<StructureSection load='' size='350' side='right' scene='2eyq/Domainscolorsflabe/3' caption=''>
-	The <scene name='~~2eyq~~/~~Domainscolorsflabe~~/3'>~~initial scene~~</scene> shows the domains of Mfd in the conformation of the apo-enzyme.<ref>DOI:10.1016/j.cell.2005.11.045</ref> The UvrA interaction site (on domain 2) is occluded by domain 7. The translocase domains (domain 5 and domain 6), through interactions with domains 1 and 3, are locked in an inactive conformation, preventing the typical hinge motion of translocases when they bind and hydrolyze ATP while moving along DNA.	+	The initial scene (switch to <scene name='46/460252/Apo/1'>cartoon</scene>) shows the domains of Mfd in the conformation of the apo-enzyme.<ref>DOI:10.1016/j.cell.2005.11.045</ref> The UvrA interaction site (on domain 2) is occluded by domain 7. The translocase domains (domain 5 and domain 6), through interactions with domains 1 and 3, are locked in an inactive conformation, preventing the typical hinge motion of translocases when they bind and hydrolyze ATP while moving along DNA.

	[[Image:Mfd domains.JPG\|thumb\|left]]		[[Image:Mfd domains.JPG\|thumb\|left]]