6z2b - Revision history

OCA at 13:40, 24 January 2024

OCA — Wed, 24 Jan 2024 13:40:26 GMT

←Older revision		Revision as of 13:40, 24 January 2024
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	<StructureSection load='6z2b' size='340' side='right'caption='[[6z2b]], [[Resolution\|resolution]] 2.14Å' scene=''>		<StructureSection load='6z2b' size='340' side='right'caption='[[6z2b]], [[Resolution\|resolution]] 2.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6z2b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z2b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2B 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]] 2.138Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rnmV, B4109_0079, B4114_0027, D9548_05595, TGS27_1231 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1422 ATCC 12980])</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/Ribonuclease_M5 Ribonuclease M5], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.8 3.1.26.8]~~ </~~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=6z2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2b OCA], [https://pdbe.org/6z2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2b RCSB], [https://www.ebi.ac.uk/pdbsum/6z2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2b 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=6z2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2b OCA], [https://pdbe.org/6z2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2b RCSB], [https://www.ebi.ac.uk/pdbsum/6z2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A087LGV4_GEOSE A0A087LGV4_GEOSE]] Required for correct processing of both the 5' and 3' ends of 5S rRNA precursor. Cleaves both sides of a double-stranded region yielding mature 5S rRNA in one step.[HAMAP-Rule:MF_01469]	+	[https://www.uniprot.org/uniprot/A0A087LGV4_GEOSE A0A087LGV4_GEOSE] Required for correct processing of both the 5' and 3' ends of 5S rRNA precursor. Cleaves both sides of a double-stranded region yielding mature 5S rRNA in one step.[HAMAP-Rule:MF_01469]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6z2b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6z2b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonuclease M5]]~~	+	[[Category: Catala M]]
-	[[Category: Catala, M]]	+	[[Category: Oerum S]]
-	[[Category: Oerum, S]]	+	[[Category: Tisne C]]
-	[[Category: Tisne, C]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Magnesium binding]]~~	+
-	~~[[Category: Ribonuclease]]~~	+
-	~~[[Category: Ribosomal rna ribonuclease]]~~	+
-	~~[[Category: Rnase m5]]~~	+
-	~~[[Category: Toprim domain~~]]	+

OCA at 14:08, 17 November 2021

OCA — Wed, 17 Nov 2021 14:08:56 GMT

←Older revision		Revision as of 14:08, 17 November 2021
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	==Toprim domain of RNase M5 bound with two Mg2+ ions==		==Toprim domain of RNase M5 bound with two Mg2+ ions==
-	<StructureSection load='6z2b' size='340' side='right'caption='[[6z2b]]' scene=''>	+	<StructureSection load='6z2b' size='340' side='right'caption='[[6z2b]], [[Resolution\|resolution]] 2.14Å' 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=6Z2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z2b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2B 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=6z2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2b OCA], [https://pdbe.org/6z2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2b RCSB], [https://www.ebi.ac.uk/pdbsum/6z2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2b 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">rnmV, B4109_0079, B4114_0027, D9548_05595, TGS27_1231 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_M5 Ribonuclease M5], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.8 3.1.26.8] </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=6z2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2b OCA], [https://pdbe.org/6z2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2b RCSB], [https://www.ebi.ac.uk/pdbsum/6z2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A087LGV4_GEOSE A0A087LGV4_GEOSE]] Required for correct processing of both the 5' and 3' ends of 5S rRNA precursor. Cleaves both sides of a double-stranded region yielding mature 5S rRNA in one step.[HAMAP-Rule:MF_01469]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	All species transcribe ribosomal RNA in an immature form that requires several enzymes for processing into mature rRNA. The number and types of enzymes utilized for these processes vary greatly between different species. In low G + C Gram-positive bacteria including Bacillus subtilis and Geobacillus stearothermophilus, the endoribonuclease (RNase) M5 performs the final step in 5S rRNA maturation, by removing the 3'- and 5'-extensions from precursor (pre) 5S rRNA. This cleavage activity requires initial complex formation between the pre-rRNA and a ribosomal protein, uL18, making the full M5 substrate a ribonucleoprotein particle (RNP). M5 contains a catalytic N-terminal Toprim domain and an RNA-binding C-terminal domain, respectively, shown to assist in processing and binding of the RNP. Here, we present structural data that show how two Mg(2+) ions are accommodated in the active site pocket of the catalytic Toprim domain and investigate the importance of these ions for catalysis. We further perform solution studies that support the previously proposed 3'-before-5' order of removal of the pre-5S rRNA extensions and map the corresponding M5 structural rearrangements during catalysis.
		+
		+	Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation.,Oerum S, Catala M, Bourguet M, Gilet L, Barraud P, Cianferani S, Condon C, Tisne C RNA Biol. 2021 Feb 23:1-11. doi: 10.1080/15476286.2021.1885896. PMID:33541205<ref>PMID:33541205</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6z2b" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Catala M]]	+	[[Category: Ribonuclease M5]]
-	[[Category: Oerum S]]	+	[[Category: Catala, M]]
-	[[Category: Tisne C]]	+	[[Category: Oerum, S]]
		+	[[Category: Tisne, C]]
		+	[[Category: Hydrolase]]
		+	[[Category: Magnesium binding]]
		+	[[Category: Ribonuclease]]
		+	[[Category: Ribosomal rna ribonuclease]]
		+	[[Category: Rnase m5]]
		+	[[Category: Toprim domain]]

OCA at 06:43, 17 March 2021

OCA — Wed, 17 Mar 2021 06:43:44 GMT

←Older revision		Revision as of 06:43, 17 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6z2b is ~~ON HOLD until Paper Publication~~	+	==Toprim domain of RNase M5 bound with two Mg2+ ions==
-		+	<StructureSection load='6z2b' size='340' side='right'caption='[[6z2b]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2B FirstGlance]. <br>
-	~~Description~~:	+	</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=6z2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2b OCA], [https://pdbe.org/6z2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2b RCSB], [https://www.ebi.ac.uk/pdbsum/6z2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2b ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Catala M]]
		+	[[Category: Oerum S]]
		+	[[Category: Tisne C]]

OCA at 05:18, 3 June 2020

OCA — Wed, 03 Jun 2020 05:18:23 GMT

←Older revision		Revision as of 05:18, 3 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6z2b is ON HOLD	+	The entry 6z2b is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6z2b" [edit=sysop:move=sysop]

OCA — Wed, 27 May 2020 05:02:32 GMT

Protected "6z2b" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:02, 27 May 2020

OCA: New page: '''Unreleased structure''' The entry 6z2b is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 May 2020 05:02:30 GMT

New page: '''Unreleased structure''' The entry 6z2b is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6z2b is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]