6is0 - Revision history

OCA at 14:32, 6 March 2024

2024-03-06T14:32:55Z

←Older revision		Revision as of 14:32, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CAPAM_DANRE CAPAM_DANRE] Cap-specific adenosine methyltransferase that catalyzes formation of N(6),2'-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs (PubMed:30467178).<ref>PMID:30467178</ref>		[https://www.uniprot.org/uniprot/CAPAM_DANRE CAPAM_DANRE] Cap-specific adenosine methyltransferase that catalyzes formation of N(6),2'-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs (PubMed:30467178).<ref>PMID:30467178</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	N (6)-methyladenosine (m(6)A), a major modification of mRNAs, plays critical roles in RNA metabolism and function. In addition to the internal m(6)A, N (6), 2'-O-dimethyladenosine (m(6)Am) is present at the transcription start nucleotide of capped mRNAs in vertebrates. However, its biogenesis and functional role remain elusive. Using a reverse genetics approach, we identified PCIF1, a factor that interacts with the Ser5-phosphorylated C-terminal domain of RNA polymerase II, as cap-specific adenosine methyltransferase (CAPAM) responsible for N (6)-methylation of m(6)Am. Crystal structure of CAPAM in complex with substrates revealed the molecular basis of cap-specific m(6)A formation. A transcriptome-wide analysis revealed that N (6)-methylation of m(6)Am promotes the translation of capped mRNAs. Thus, a cap-specific m(6)A writer promotes translation of mRNAs starting from m(6)Am.
-
-	Cap-specific terminal N (6)-methylation of RNA by an RNA polymerase II-associated methyltransferase.,Akichika S, Hirano S, Shichino Y, Suzuki T, Nishimasu H, Ishitani R, Sugita A, Hirose Y, Iwasaki S, Nureki O, Suzuki T Science. 2018 Nov 22. pii: science.aav0080. doi: 10.1126/science.aav0080. PMID:30467178<ref>PMID:30467178</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6is0" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:52, 22 November 2023

2023-11-22T09:52:09Z

←Older revision		Revision as of 09:52, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6is0' size='340' side='right'caption='[[6is0]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6is0' size='340' side='right'caption='[[6is0]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6is0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IS0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6IS0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6is0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IS0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IS0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>~~</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]] 1.8Å</td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pcif1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])~~</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=6is0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6is0 OCA], [https://pdbe.org/6is0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6is0 RCSB], [https://www.ebi.ac.uk/pdbsum/6is0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6is0 ProSAT]</span></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=6is0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6is0 OCA], [~~http~~://pdbe.org/6is0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6is0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6is0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6is0 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CAPAM_DANRE CAPAM_DANRE] Cap-specific adenosine methyltransferase that catalyzes formation of N(6),2'-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs (PubMed:30467178).<ref>PMID:30467178</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hirano, S]]	+	[[Category: Synthetic construct]]
-	[[Category: Ishitani, R]]	+	[[Category: Hirano S]]
-	[[Category: Nishimasu, H]]	+	[[Category: Ishitani R]]
-	[[Category: Nureki, O]]	+	[[Category: Nishimasu H]]
-	~~[[Category: M6a]]~~	+	[[Category: Nureki O]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: N6-methyladenosine]]~~	+
-	~~[[Category: Rna methylation]]~~	+
-	~~[[Category: Transferase-rna complex~~]]	+

OCA at 20:40, 28 October 2020

2020-10-28T20:40:11Z

←Older revision		Revision as of 20:40, 28 October 2020
Line 1:		Line 1:

	==Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA==		==Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA==
-	<StructureSection load='6is0' size='340' side='right' caption='[[6is0]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='6is0' size='340' side='right'caption='[[6is0]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6is0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IS0 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IS0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6is0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IS0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6IS0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></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=6is0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6is0 OCA], [http://pdbe.org/6is0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6is0 RCSB], [http://www.ebi.ac.uk/pdbsum/6is0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6is0 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pcif1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=6is0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6is0 OCA], [http://pdbe.org/6is0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6is0 RCSB], [http://www.ebi.ac.uk/pdbsum/6is0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6is0 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
		+	[[Category: Large Structures]]
	[[Category: Hirano, S]]		[[Category: Hirano, S]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 06:49, 5 December 2018

2018-12-05T06:49:28Z

←Older revision		Revision as of 06:49, 5 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6is0 is ~~ON HOLD~~	+	==Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA==
		+	<StructureSection load='6is0' size='340' side='right' caption='[[6is0]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6is0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IS0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IS0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></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=6is0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6is0 OCA], [http://pdbe.org/6is0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6is0 RCSB], [http://www.ebi.ac.uk/pdbsum/6is0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6is0 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N (6)-methyladenosine (m(6)A), a major modification of mRNAs, plays critical roles in RNA metabolism and function. In addition to the internal m(6)A, N (6), 2'-O-dimethyladenosine (m(6)Am) is present at the transcription start nucleotide of capped mRNAs in vertebrates. However, its biogenesis and functional role remain elusive. Using a reverse genetics approach, we identified PCIF1, a factor that interacts with the Ser5-phosphorylated C-terminal domain of RNA polymerase II, as cap-specific adenosine methyltransferase (CAPAM) responsible for N (6)-methylation of m(6)Am. Crystal structure of CAPAM in complex with substrates revealed the molecular basis of cap-specific m(6)A formation. A transcriptome-wide analysis revealed that N (6)-methylation of m(6)Am promotes the translation of capped mRNAs. Thus, a cap-specific m(6)A writer promotes translation of mRNAs starting from m(6)Am.

-	~~Authors: Hirano~~, S., ~~Nishimasu~~, H., Ishitani, R., ~~Nureki~~, O.	+	Cap-specific terminal N (6)-methylation of RNA by an RNA polymerase II-associated methyltransferase.,Akichika S, Hirano S, Shichino Y, Suzuki T, Nishimasu H, Ishitani R, Sugita A, Hirose Y, Iwasaki S, Nureki O, Suzuki T Science. 2018 Nov 22. pii: science.aav0080. doi: 10.1126/science.aav0080. PMID:30467178<ref>PMID:30467178</ref>

-	~~Description: Crystal structure~~ of the ~~zebrafish cap~~-~~specific adenosine methyltransferase bound to SAH and m7G~~-~~capped RNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Nureki, O]]~~	+	<div class="pdbe-citations 6is0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Hirano, S]]		[[Category: Hirano, S]]
-	[[Category: Nishimasu, H]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
		+	[[Category: Nishimasu, H]]
		+	[[Category: Nureki, O]]
		+	[[Category: M6a]]
		+	[[Category: Methyltransferase]]
		+	[[Category: N6-methyladenosine]]
		+	[[Category: Rna methylation]]
		+	[[Category: Transferase-rna complex]]

OCA: Protected "6is0" [edit=sysop:move=sysop]

2018-12-02T18:54:40Z

Protected "6is0" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:54, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6is0 is ON HOLD Authors: Hirano, S., Nishimasu, H., Ishitani, R., Nureki, O. Description: Crystal structure of the zebrafish cap-specific adenosine...

2018-12-02T18:54:38Z

New page: '''Unreleased structure''' The entry 6is0 is ON HOLD Authors: Hirano, S., Nishimasu, H., Ishitani, R., Nureki, O. Description: Crystal structure of the zebrafish cap-specific adenosine...

New page

'''Unreleased structure'''

The entry 6is0 is ON HOLD

Authors: Hirano, S., Nishimasu, H., Ishitani, R., Nureki, O.

Description: Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA
[[Category: Unreleased Structures]]
[[Category: Nureki, O]]
[[Category: Hirano, S]]
[[Category: Nishimasu, H]]
[[Category: Ishitani, R]]