5hfz - Revision history

OCA at 12:32, 6 March 2024

2024-03-06T12:32:13Z

←Older revision		Revision as of 12:32, 6 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>		[https://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the prt locus upstream of pho1 to produce a long noncoding (lnc) prt RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO4 mark (as in S7A) derepresses Pho1 expression, and inability to place a Thr4-PO4 mark (as in T4A) hyper-represses Pho1 in phosphate replete cells. Here we find that basal pho1 expression from the prt-pho1 locus is inversely correlated with the activity of the prt promoter, which resides in a 110-nucleotide DNA segment preceding the prt transcription start site. CTD mutations S7A and T4A had no effect on the activity of the prt promoter or the pho1 promoter, suggesting that S7A and T4A affect post-initiation events in prt lncRNA synthesis that make it less and more repressive of pho1, respectively. prt lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the prt lncRNA caused hyper-repression of pho1 in phosphate replete cells, concomitant with increased levels of the prt transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 A crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m(6)A-modified RNA.
-
-	Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast.,Chatterjee D, Sanchez AM, Goldgur Y, Shuman S, Schwer B RNA. 2016 Jul;22(7):1011-25. doi: 10.1261/rna.056515.116. Epub 2016 May 10. PMID:27165520<ref>PMID:27165520</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5hfz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:34, 9 August 2023

2023-08-09T07:34:55Z

←Older revision		Revision as of 07:34, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='5hfz' size='340' side='right'caption='[[5hfz]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='5hfz' size='340' side='right'caption='[[5hfz]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hfz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HFZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HFZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hfz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HFZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HFZ FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~mmi1~~, ~~SPCC736.12c (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=284812 Fission yeast])~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.96Å</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5hfz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hfz OCA], [https://pdbe.org/5hfz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hfz RCSB], [https://www.ebi.ac.uk/pdbsum/5hfz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hfz ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5hfz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hfz OCA], [https://pdbe.org/5hfz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hfz RCSB], [https://www.ebi.ac.uk/pdbsum/5hfz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hfz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO]] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>	+	[https://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chatterjee, D~~]]	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	[[Category: ~~Goldgur, Y~~]]	+	[[Category: Chatterjee D]]
-	[[Category: ~~Shuman, S~~]]	+	[[Category: Goldgur Y]]
-	[[Category: ~~Rna binding]]~~	+	[[Category: Shuman S]]
-	~~[[Category: Rna binding protein~~]]	+

OCA at 03:38, 2 July 2021

2021-07-02T03:38:54Z

←Older revision		Revision as of 03:38, 2 July 2021
Line 3:		Line 3:
	<StructureSection load='5hfz' size='340' side='right'caption='[[5hfz]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='5hfz' size='340' side='right'caption='[[5hfz]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hfz]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HFZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HFZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hfz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HFZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HFZ FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mmi1, SPCC736.12c ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mmi1, SPCC736.12c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5hfz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hfz OCA], [~~http~~://pdbe.org/5hfz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hfz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hfz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hfz ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5hfz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hfz OCA], [https://pdbe.org/5hfz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hfz RCSB], [https://www.ebi.ac.uk/pdbsum/5hfz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hfz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO]] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>	+	[[https://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO]] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the prt locus upstream of pho1 to produce a long noncoding (lnc) prt RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO4 mark (as in S7A) derepresses Pho1 expression, and inability to place a Thr4-PO4 mark (as in T4A) hyper-represses Pho1 in phosphate replete cells. Here we find that basal pho1 expression from the prt-pho1 locus is inversely correlated with the activity of the prt promoter, which resides in a 110-nucleotide DNA segment preceding the prt transcription start site. CTD mutations S7A and T4A had no effect on the activity of the prt promoter or the pho1 promoter, suggesting that S7A and T4A affect post-initiation events in prt lncRNA synthesis that make it less and more repressive of pho1, respectively. prt lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the prt lncRNA caused hyper-repression of pho1 in phosphate replete cells, concomitant with increased levels of the prt transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 A crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m(6)A-modified RNA.
		+
		+	Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast.,Chatterjee D, Sanchez AM, Goldgur Y, Shuman S, Schwer B RNA. 2016 Jul;22(7):1011-25. doi: 10.1261/rna.056515.116. Epub 2016 May 10. PMID:27165520<ref>PMID:27165520</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5hfz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:04, 20 May 2020

2020-05-20T07:04:47Z

←Older revision		Revision as of 07:04, 20 May 2020
Line 1:		Line 1:
		+
	==Mmi1 YTH domain==		==Mmi1 YTH domain==
-	<StructureSection load='5hfz' size='340' side='right' caption='[[5hfz]], [[Resolution\|resolution]] 1.96Å' scene=''>	+	<StructureSection load='5hfz' size='340' side='right'caption='[[5hfz]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hfz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HFZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HFZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hfz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HFZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HFZ FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5hfz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hfz OCA], [http://pdbe.org/5hfz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hfz RCSB], [http://www.ebi.ac.uk/pdbsum/5hfz PDBsum]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mmi1, SPCC736.12c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5hfz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hfz OCA], [http://pdbe.org/5hfz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hfz RCSB], [http://www.ebi.ac.uk/pdbsum/5hfz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hfz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 13:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Fission yeast]]
		+	[[Category: Large Structures]]
	[[Category: Chatterjee, D]]		[[Category: Chatterjee, D]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
-	[[Category: Fission yeast]]
	[[Category: Rna binding]]		[[Category: Rna binding]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]

OCA at 17:29, 10 February 2016

2016-02-10T17:29:30Z

←Older revision		Revision as of 17:29, 10 February 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Mmi1 YTH domain==
-		+	<StructureSection load='5hfz' size='340' side='right' caption='[[5hfz]], [[Resolution\|resolution]] 1.96Å' scene=''>
-	~~The entry~~ 5hfz is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5hfz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HFZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HFZ FirstGlance]. <br>
-	~~Authors~~: ~~Chatterjee~~, D., ~~Goldgur~~, Y., ~~Shuman, S~~.	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5hfz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hfz OCA], [http://pdbe.org/5hfz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hfz RCSB], [http://www.ebi.ac.uk/pdbsum/5hfz PDBsum]</span></td></tr>
-		+	</table>
-	~~Description: Mmi1 YTH domain~~	+	== Function ==
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	[[http://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO]] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Chatterjee, D]]		[[Category: Chatterjee, D]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
		+	[[Category: Fission yeast]]
		+	[[Category: Rna binding]]
		+	[[Category: Rna binding protein]]

OCA: Protected "5hfz" [edit=sysop:move=sysop]

2016-01-13T19:00:09Z

Protected "5hfz" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:00, 13 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hfz is ON HOLD Authors: Chatterjee, D., Goldgur, Y., Shuman, S. Description: Mmi1 YTH domain Category: Unreleased Structures [[Category: Chatt...

2016-01-13T19:00:07Z

New page: '''Unreleased structure''' The entry 5hfz is ON HOLD Authors: Chatterjee, D., Goldgur, Y., Shuman, S. Description: Mmi1 YTH domain Category: Unreleased Structures [[Category: Chatt...

New page

'''Unreleased structure'''

The entry 5hfz is ON HOLD

Authors: Chatterjee, D., Goldgur, Y., Shuman, S.

Description: Mmi1 YTH domain
[[Category: Unreleased Structures]]
[[Category: Chatterjee, D]]
[[Category: Goldgur, Y]]
[[Category: Shuman, S]]