5izo - Revision history

OCA at 10:40, 6 September 2023

OCA — Wed, 06 Sep 2023 10:40:07 GMT

←Older revision		Revision as of 10:40, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5izo' size='340' side='right'caption='[[5izo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5izo' size='340' side='right'caption='[[5izo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IZO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</scene~~>, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.95Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5ipp\|5ipp]], [[5iuf\|5iuf]], [[5j2z\|5j2z]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">nrnA, ytqI, BSU29250 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])~~</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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [https://pdbe.org/5izo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [https://www.ebi.ac.uk/pdbsum/5izo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</span></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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [~~http~~://pdbe.org/5izo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5izo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NRNA_BACSU NRNA_BACSU]] Bifunctional enzyme which has both oligoribonuclease and pAp-phosphatase activities. Degrades RNA and DNA oligonucleotides with a length of 5 nucleotides and shorter, with a preference for 3-mers. Directionality is controversial; shown to degrade 5-mers and less in a 3' to 5' direction (PubMed:17586819), and 11-mers in a 5' to 3' direction (PubMed:21087930). Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP.<ref>PMID:17586819</ref> <ref>PMID:21087930</ref> <ref>PMID:22114320</ref>	+	[https://www.uniprot.org/uniprot/NRNA_BACSU NRNA_BACSU] Bifunctional enzyme which has both oligoribonuclease and pAp-phosphatase activities. Degrades RNA and DNA oligonucleotides with a length of 5 nucleotides and shorter, with a preference for 3-mers. Directionality is controversial; shown to degrade 5-mers and less in a 3' to 5' direction (PubMed:17586819), and 11-mers in a 5' to 3' direction (PubMed:21087930). Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP.<ref>PMID:17586819</ref> <ref>PMID:21087930</ref> <ref>PMID:22114320</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Malhotra, A]]	+	[[Category: Malhotra A]]
-	[[Category: Nelersa~~, C M~~]]	+	[[Category: Nelersa CM]]
-	[[Category: Schmier~~, B J]]~~	+	[[Category: Schmier BJ]]
-	~~[[Category: Abortive transcript]]~~	+
-	~~[[Category: B. subtili]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nanorna]]~~	+
-	~~[[Category: Pap phosphatase]]~~	+
-	~~[[Category: Rna degradation]]~~	+
-	~~[[Category: Rnase~~]]	+

OCA at 11:52, 25 December 2019

OCA — Wed, 25 Dec 2019 11:52:18 GMT

←Older revision		Revision as of 11:52, 25 December 2019
Line 1:		Line 1:

	==Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site==		==Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site==
-	<StructureSection load='5izo' size='340' side='right' caption='[[5izo]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5izo' size='340' side='right'caption='[[5izo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IZO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IZO FirstGlance]. <br>
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Bacsu]]		[[Category: Bacsu]]
		+	[[Category: Large Structures]]
	[[Category: Malhotra, A]]		[[Category: Malhotra, A]]
	[[Category: Nelersa, C M]]		[[Category: Nelersa, C M]]

OCA at 09:40, 13 February 2019

OCA — Wed, 13 Feb 2019 09:40:10 GMT

←Older revision		Revision as of 09:40, 13 February 2019
Line 3:		Line 3:
	<StructureSection load='5izo' size='340' side='right' caption='[[5izo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5izo' size='340' side='right' caption='[[5izo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IZO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipp\|5ipp]], [[5iuf\|5iuf]], [[5j2z\|5j2z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipp\|5ipp]], [[5iuf\|5iuf]], [[5j2z\|5j2z]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nrnA, ytqI, BSU29250 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [http://pdbe.org/5izo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [http://www.ebi.ac.uk/pdbsum/5izo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</span></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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [http://pdbe.org/5izo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [http://www.ebi.ac.uk/pdbsum/5izo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</span></td></tr>
	</table>		</table>
Line 12:		Line 13:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~The final step in RNA degradation is the hydrolysis of~~ RNA fragments ~~five~~ nucleotides ~~or less~~ in length ~~(nanoRNA) to mononucleotides~~. ~~In Escherichia coli this step is carried out by oligoribonuclease~~ (~~Orn~~), a ~~DEDD~~-~~family exoribonuclease~~ that is ~~conserved throughout eukaryotes. However~~, ~~many bacteria lack Orn homologs, and an unrelated DHH~~-~~family phosphoesterase~~, ~~NrnA, has recently been identified as one of~~ the ~~enzymes responsible for nanoRNA degradation in Bacillus subtilis~~. ~~To understand its mechanism~~ of ~~action, B.~~ subtilis NrnA ~~was purified and crystallized at room temperature using~~ the ~~hanging~~-~~drop vapor~~-~~diffusion method with PEG 4000, PEG 3350 or PEG MME 2000 as precipitant~~. ~~The crystals belonged~~ to the ~~primitive monoclinic space group P2(1)~~, ~~with unit-cell parameters~~ a ~~= 50.62, b = 121.~~3, ~~c = 123.4 A, alpha = 90, beta = 91.31, gamma = 90 degrees~~ .	+	NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3' --> 5' exonuclease, but we show here that NrnA is bidirectional, degrading 2-5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5' --> 3' DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3' --> 5' activity.

-	~~Purification and crystallization~~ of Bacillus ~~subtilis~~ NrnA~~, a novel enzyme involved in nanoRNA degradation~~.,Nelersa CM~~, Schmier BJ~~, Malhotra A ~~Acta Crystallogr Sect F Struct Biol Cryst Commun~~. ~~2011 Oct 1~~;67(~~Pt 10~~):~~1235-8~~., doi: 10.~~1107~~/~~S1744309111026509. Epub 2011 Sep 29~~. PMID:~~22102036~~<ref>PMID:~~22102036~~</ref>	+	Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.,Schmier BJ, Nelersa CM, Malhotra A Sci Rep. 2017 Sep 11;7(1):11085. doi: 10.1038/s41598-017-09403-x. PMID:28894100<ref>PMID:28894100</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	<div class="pdbe-citations 5izo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5izo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Malhotra, A]]		[[Category: Malhotra, A]]
	[[Category: Nelersa, C M]]		[[Category: Nelersa, C M]]

OCA at 07:55, 13 November 2017

OCA — Mon, 13 Nov 2017 07:55:34 GMT

←Older revision		Revision as of 07:55, 13 November 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5izo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5izo" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ribonuclease\|Ribonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:19, 6 October 2017

OCA — Fri, 06 Oct 2017 07:19:52 GMT

←Older revision		Revision as of 07:19, 6 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5izo is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site==
		+	<StructureSection load='5izo' size='340' side='right' caption='[[5izo]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IZO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipp\|5ipp]], [[5iuf\|5iuf]], [[5j2z\|5j2z]]</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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [http://pdbe.org/5izo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [http://www.ebi.ac.uk/pdbsum/5izo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NRNA_BACSU NRNA_BACSU]] Bifunctional enzyme which has both oligoribonuclease and pAp-phosphatase activities. Degrades RNA and DNA oligonucleotides with a length of 5 nucleotides and shorter, with a preference for 3-mers. Directionality is controversial; shown to degrade 5-mers and less in a 3' to 5' direction (PubMed:17586819), and 11-mers in a 5' to 3' direction (PubMed:21087930). Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP.<ref>PMID:17586819</ref> <ref>PMID:21087930</ref> <ref>PMID:22114320</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The final step in RNA degradation is the hydrolysis of RNA fragments five nucleotides or less in length (nanoRNA) to mononucleotides. In Escherichia coli this step is carried out by oligoribonuclease (Orn), a DEDD-family exoribonuclease that is conserved throughout eukaryotes. However, many bacteria lack Orn homologs, and an unrelated DHH-family phosphoesterase, NrnA, has recently been identified as one of the enzymes responsible for nanoRNA degradation in Bacillus subtilis. To understand its mechanism of action, B. subtilis NrnA was purified and crystallized at room temperature using the hanging-drop vapor-diffusion method with PEG 4000, PEG 3350 or PEG MME 2000 as precipitant. The crystals belonged to the primitive monoclinic space group P2(1), with unit-cell parameters a = 50.62, b = 121.3, c = 123.4 A, alpha = 90, beta = 91.31, gamma = 90 degrees .

-	~~Authors: Schmier~~, ~~B.J~~., ~~Malhotra~~, A., ~~Nelersa, C~~.M.	+	Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation.,Nelersa CM, Schmier BJ, Malhotra A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1235-8., doi: 10.1107/S1744309111026509. Epub 2011 Sep 29. PMID:22102036<ref>PMID:22102036</ref>

-	~~Description: Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at~~ the ~~active site~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[~~Category: Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5izo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Malhotra, A]]		[[Category: Malhotra, A]]
-	[[Category: Schmier, B.J]]	+	[[Category: Nelersa, C M]]
-	[[Category: ~~Nelersa, C~~.M]]	+	[[Category: Schmier, B J]]
		+	[[Category: Abortive transcript]]
		+	[[Category: B. subtili]]
		+	[[Category: Exonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nanorna]]
		+	[[Category: Pap phosphatase]]
		+	[[Category: Rna degradation]]
		+	[[Category: Rnase]]

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

OCA — Wed, 11 May 2016 01:13:12 GMT

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

←Older revision

Revision as of 01:13, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5izo is ON HOLD until Paper Publication Authors: Schmier, B.J., Malhotra, A., Nelersa, C.M. Description: Bacillus NanoRNase A (H103A) + 2 divalent ...

OCA — Wed, 11 May 2016 01:13:11 GMT

New page: '''Unreleased structure''' The entry 5izo is ON HOLD until Paper Publication Authors: Schmier, B.J., Malhotra, A., Nelersa, C.M. Description: Bacillus NanoRNase A (H103A) + 2 divalent ...

New page

'''Unreleased structure'''

The entry 5izo is ON HOLD until Paper Publication

Authors: Schmier, B.J., Malhotra, A., Nelersa, C.M.

Description: Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site
[[Category: Unreleased Structures]]
[[Category: Malhotra, A]]
[[Category: Schmier, B.J]]
[[Category: Nelersa, C.M]]