7dcy - Revision history

OCA at 16:30, 29 November 2023

OCA — Wed, 29 Nov 2023 16:30:55 GMT

←Older revision		Revision as of 16:30, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7dcy' size='340' side='right'caption='[[7dcy]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='7dcy' size='340' side='right'caption='[[7dcy]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7dcy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Mycge Mycge~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dcy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplasma_genitalium_G37 Mycoplasma genitalium G37]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.972Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rnr, vacB, MG104 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~243273 MYCGE])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Exoribonuclease_II Exoribonuclease II], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.1 3.1.13.1]~~ </~~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=7dcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dcy OCA], [https://pdbe.org/7dcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dcy RCSB], [https://www.ebi.ac.uk/pdbsum/7dcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dcy 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=7dcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dcy OCA], [https://pdbe.org/7dcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dcy RCSB], [https://www.ebi.ac.uk/pdbsum/7dcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dcy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RNR_MYCGE RNR_MYCGE]] 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.	+	[https://www.uniprot.org/uniprot/RNR_MYCGE RNR_MYCGE] 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7dcy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7dcy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Exoribonuclease II]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mycge~~]]	+	[[Category: Mycoplasma genitalium G37]]
-	[[Category: Abula, A]]	+	[[Category: Abula A]]
-	[[Category: Chen, Q]]	+	[[Category: Chen Q]]
-	[[Category: Ji, X]]	+	[[Category: Ji X]]
-	[[Category: Li, T]]	+	[[Category: Li T]]
-	[[Category: Li, X]]	+	[[Category: Li X]]
-	[[Category: Quan, X]]	+	[[Category: Quan X]]
-	[[Category: Yang, T]]	+	[[Category: Yang T]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rna 2'-o-methylation sensitive]]~~	+
-	~~[[Category: Rna hydrolase~~]]	+

OCA at 07:02, 14 April 2021

OCA — Wed, 14 Apr 2021 07:02:24 GMT

←Older revision		Revision as of 07:02, 14 April 2021
Line 1:		Line 1:

	==Apo form of Mycoplasma genitalium RNase R==		==Apo form of Mycoplasma genitalium RNase R==
-	<StructureSection load='7dcy' size='340' side='right'caption='[[7dcy]]' scene=''>	+	<StructureSection load='7dcy' size='340' side='right'caption='[[7dcy]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dcy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycge Mycge]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCY FirstGlance]. <br>
-	</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=7dcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dcy OCA], [https://pdbe.org/7dcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dcy RCSB], [https://www.ebi.ac.uk/pdbsum/7dcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dcy ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnr, vacB, MG104 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243273 MYCGE])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exoribonuclease_II Exoribonuclease II], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.1 3.1.13.1] </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=7dcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dcy OCA], [https://pdbe.org/7dcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dcy RCSB], [https://www.ebi.ac.uk/pdbsum/7dcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dcy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/RNR_MYCGE RNR_MYCGE]] 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA 2'-O-methylation is widely distributed and plays important roles in various cellular processes. Mycoplasma genitalium RNase R (MgR), a prokaryotic member of the RNase II/RNB family, is a 3'-5' exoribonuclease and is particularly sensitive to RNA 2'-O-methylation. However, how RNase R interacts with various RNA species and exhibits remarkable sensitivity to substrate 2'-O-methyl modifications remains elusive. Here we report high-resolution crystal structures of MgR in apo form and in complex with various RNA substrates. The structural data together with extensive biochemical analysis quantitively illustrate MgR's ribonuclease activity and significant sensitivity to RNA 2'-O-methylation. Comparison to its related homologs reveals an exquisite mechanism for the recognition and degradation of RNA substrates. Through structural and mutagenesis studies, we identified proline 277 to be responsible for the significant sensitivity of MgR to RNA 2'-O-methylation within the RNase II/RNB family. We also generated several MgR variants with modulated activities. Our work provides a mechanistic understanding of MgR activity that can be harnessed as a powerful RNA analytical tool that will open up a new venue for RNA 2'-O-methylations research in biological and clinical samples.
		+
		+	Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.,Abula A, Li X, Quan X, Yang T, Liu Y, Guo H, Li T, Ji X Nucleic Acids Res. 2021 Mar 31. pii: 6206732. doi: 10.1093/nar/gkab202. PMID:33788943<ref>PMID:33788943</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dcy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Exoribonuclease II]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abula A]]	+	[[Category: Mycge]]
-	[[Category: Chen Q]]	+	[[Category: Abula, A]]
-	[[Category: Ji X]]	+	[[Category: Chen, Q]]
-	[[Category: Li T]]	+	[[Category: Ji, X]]
-	[[Category: Li X]]	+	[[Category: Li, T]]
-	[[Category: Quan X]]	+	[[Category: Li, X]]
-	[[Category: Yang T]]	+	[[Category: Quan, X]]
		+	[[Category: Yang, T]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rna 2'-o-methylation sensitive]]
		+	[[Category: Rna hydrolase]]

OCA at 06:46, 17 March 2021

OCA — Wed, 17 Mar 2021 06:46:58 GMT

←Older revision		Revision as of 06:46, 17 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7dcy ~~is ON HOLD~~	+	==Apo form of Mycoplasma genitalium RNase R==
-		+	<StructureSection load='7dcy' size='340' side='right'caption='[[7dcy]]' scene=''>
-	~~Authors~~: ~~Abula, A~~.~~, Quan, X~~., ~~Li, X~~.~~, Yang, T~~., ~~Li, T~~., ~~Chen~~, Q., ~~Ji, X~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCY FirstGlance]. <br>
-	~~Description: Apo form of Mycoplasma genitalium RNase R~~	+	</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=7dcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dcy OCA], [https://pdbe.org/7dcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dcy RCSB], [https://www.ebi.ac.uk/pdbsum/7dcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dcy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Yang, T~~]]	+	__TOC__
-	[[Category: ~~Li, X~~]]	+	</StructureSection>
-	[[Category: ~~Li, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ji, X~~]]	+	[[Category: Abula A]]
-	[[Category: ~~Chen, Q~~]]	+	[[Category: Chen Q]]
-	[[Category: ~~Abula, A~~]]	+	[[Category: Ji X]]
-	[[Category: ~~Quan, X~~]]	+	[[Category: Li T]]
		+	[[Category: Li X]]
		+	[[Category: Quan X]]
		+	[[Category: Yang T]]

OCA: Protected "7dcy" [edit=sysop:move=sysop]

OCA — Wed, 04 Nov 2020 05:30:51 GMT

Protected "7dcy" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:30, 4 November 2020

OCA: New page: '''Unreleased structure''' The entry 7dcy is ON HOLD Authors: Abula, A., Quan, X., Li, X., Yang, T., Li, T., Chen, Q., Ji, X. Description: Apo form of Mycoplasma genitalium RNase R [[C...

OCA — Wed, 04 Nov 2020 05:30:50 GMT

New page: '''Unreleased structure''' The entry 7dcy is ON HOLD Authors: Abula, A., Quan, X., Li, X., Yang, T., Li, T., Chen, Q., Ji, X. Description: Apo form of Mycoplasma genitalium RNase R [[C...

New page

'''Unreleased structure'''

The entry 7dcy is ON HOLD

Authors: Abula, A., Quan, X., Li, X., Yang, T., Li, T., Chen, Q., Ji, X.

Description: Apo form of Mycoplasma genitalium RNase R
[[Category: Unreleased Structures]]
[[Category: Yang, T]]
[[Category: Li, X]]
[[Category: Li, T]]
[[Category: Ji, X]]
[[Category: Chen, Q]]
[[Category: Abula, A]]
[[Category: Quan, X]]