5guq - Revision history

OCA at 09:14, 20 March 2024

OCA — Wed, 20 Mar 2024 09:14:00 GMT

←Older revision		Revision as of 09:14, 20 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/ASCHD_ZYMMA ASCHD_ZYMMA] Shows sequence-specific endoribonuclease activity towards single-stranded RNA (ssRNA), with a preference for the bond between pyrimidine and adenine nucleotides. May also have 5'-exonuclease activity.<ref>PMID:28951575</ref>		[https://www.uniprot.org/uniprot/ASCHD_ZYMMA ASCHD_ZYMMA] Shows sequence-specific endoribonuclease activity towards single-stranded RNA (ssRNA), with a preference for the bond between pyrimidine and adenine nucleotides. May also have 5'-exonuclease activity.<ref>PMID:28951575</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Activating signal cointegrator-1 homology (ASCH) domains were initially reported in human as a part of the ASC-1 transcriptional regulator, a component of a putative RNA-interacting protein complex; their presence has now been confirmed in a wide range of organisms. Here, we have determined the trigonal and monoclinic crystal structures of an ASCH domain-containing protein from Zymomonas mobilis (ZmASCH), and analyzed the structural determinants of its nucleic acid processing activity. The protein has a central beta-barrel structure with several nearby alpha-helices. Positively charged surface patches form a cleft that runs through the pocket formed between the beta-barrel and the surrounding alpha-helices. We further demonstrate by means of in vitro assays that ZmASCH binds nucleic acids, and degrades single-stranded RNAs in a magnesium ion-dependent manner with a cleavage preference for the phosphodiester bond between the pyrimidine and adenine nucleotides. ZmASCH also removes a nucleotide at the 5'-end. Mutagenesis studies, guided by molecular dynamics simulations, confirmed that three residues (Tyr47, Lys53, and Ser128) situated in the cleft contribute to nucleic acid-binding and RNA cleavage activities. These structural and biochemical studies imply that prokaryotic ASCH may function to control the cellular RNA amount.
-
-	Crystal structure of an ASCH protein from Zymomonas mobilis and its ribonuclease activity specific for single-stranded RNA.,Kim BN, Shin M, Ha SC, Park SY, Seo PW, Hofmann A, Kim JS Sci Rep. 2017 Sep 26;7(1):12303. doi: 10.1038/s41598-017-12186-w. PMID:28951575<ref>PMID:28951575</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5guq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:43, 2 August 2023

OCA — Wed, 02 Aug 2023 11:43:13 GMT

←Older revision		Revision as of 11:43, 2 August 2023
Line 1:		Line 1:

	==Crystal structure of ASCH from Zymomonas mobilis==		==Crystal structure of ASCH from Zymomonas mobilis==
-	<StructureSection load='5guq' size='340' side='right' caption='[[5guq]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5guq' size='340' side='right'caption='[[5guq]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5guq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Zymma Zymma~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5guq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_ATCC_10988 Zymomonas mobilis subsp. mobilis ATCC 10988]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GUQ FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5gus\|5gus]]</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]] 1.697Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">Zmob_0380 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=555217 ZYMMA])~~</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=5guq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5guq OCA], [https://pdbe.org/5guq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5guq RCSB], [https://www.ebi.ac.uk/pdbsum/5guq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5guq 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=5guq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5guq OCA], [~~http~~://pdbe.org/5guq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5guq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5guq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5guq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ASCHD_ZYMMA ASCHD_ZYMMA] Shows sequence-specific endoribonuclease activity towards single-stranded RNA (ssRNA), with a preference for the bond between pyrimidine and adenine nucleotides. May also have 5'-exonuclease activity.<ref>PMID:28951575</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Zymma~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ha, S C~~]]	+	[[Category: Zymomonas mobilis subsp. mobilis ATCC 10988]]
-	[[Category: ~~Kim, J S~~]]	+	[[Category: Ha SC]]
-	[[Category: ~~Park, S Y~~]]	+	[[Category: Kim JS]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Park SY]]
-	~~[[Category: Nuclease~~]]	+

OCA at 08:45, 18 July 2018

OCA — Wed, 18 Jul 2018 08:45:51 GMT

←Older revision		Revision as of 08:45, 18 July 2018
Line 3:		Line 3:
	<StructureSection load='5guq' size='340' side='right' caption='[[5guq]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5guq' size='340' side='right' caption='[[5guq]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5guq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5guq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymma Zymma]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUQ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gus\|5gus]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gus\|5gus]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Zmob_0380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=555217 ZYMMA])</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=5guq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5guq OCA], [http://pdbe.org/5guq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5guq RCSB], [http://www.ebi.ac.uk/pdbsum/5guq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5guq 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=5guq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5guq OCA], [http://pdbe.org/5guq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5guq RCSB], [http://www.ebi.ac.uk/pdbsum/5guq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5guq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Activating signal cointegrator-1 homology (ASCH) domains were initially reported in human as a part of the ASC-1 transcriptional regulator, a component of a putative RNA-interacting protein complex; their presence has now been confirmed in a wide range of organisms. Here, we have determined the trigonal and monoclinic crystal structures of an ASCH domain-containing protein from Zymomonas mobilis (ZmASCH), and analyzed the structural determinants of its nucleic acid processing activity. The protein has a central beta-barrel structure with several nearby alpha-helices. Positively charged surface patches form a cleft that runs through the pocket formed between the beta-barrel and the surrounding alpha-helices. We further demonstrate by means of in vitro assays that ZmASCH binds nucleic acids, and degrades single-stranded RNAs in a magnesium ion-dependent manner with a cleavage preference for the phosphodiester bond between the pyrimidine and adenine nucleotides. ZmASCH also removes a nucleotide at the 5'-end. Mutagenesis studies, guided by molecular dynamics simulations, confirmed that three residues (Tyr47, Lys53, and Ser128) situated in the cleft contribute to nucleic acid-binding and RNA cleavage activities. These structural and biochemical studies imply that prokaryotic ASCH may function to control the cellular RNA amount.
		+
		+	Crystal structure of an ASCH protein from Zymomonas mobilis and its ribonuclease activity specific for single-stranded RNA.,Kim BN, Shin M, Ha SC, Park SY, Seo PW, Hofmann A, Kim JS Sci Rep. 2017 Sep 26;7(1):12303. doi: 10.1038/s41598-017-12186-w. PMID:28951575<ref>PMID:28951575</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5guq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Zymma]]
	[[Category: Ha, S C]]		[[Category: Ha, S C]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]

OCA at 15:09, 5 September 2017

OCA — Tue, 05 Sep 2017 15:09:41 GMT

←Older revision		Revision as of 15:09, 5 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5guq is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of ASCH from Zymomonas mobilis==
-		+	<StructureSection load='5guq' size='340' side='right' caption='[[5guq]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~: Ha, S.C., ~~Park~~, S.Y., ~~Kim~~, J.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5guq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUQ FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of ASCH from Zymomonas mobilis~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gus\|5gus]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5guq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5guq OCA], [http://pdbe.org/5guq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5guq RCSB], [http://www.ebi.ac.uk/pdbsum/5guq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5guq ProSAT]</span></td></tr>
-	[[Category: Park, S.Y]]	+	</table>
-	[[Category: ~~Ha, S.C~~]]	+	__TOC__
-	[[Category: ~~Kim, J.S~~]]	+	</StructureSection>
		+	[[Category: Ha, S C]]
		+	[[Category: Kim, J S]]
		+	[[Category: Park, S Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclease]]

OCA at 06:51, 4 May 2017

OCA — Thu, 04 May 2017 06:51:58 GMT

←Older revision		Revision as of 06:51, 4 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5guq is ON HOLD	+	The entry 5guq is ON HOLD until Paper Publication

	Authors: Ha, S.C., Park, S.Y., Kim, J.S.		Authors: Ha, S.C., Park, S.Y., Kim, J.S.

OCA at 09:08, 9 March 2017

OCA — Thu, 09 Mar 2017 09:08:38 GMT

←Older revision		Revision as of 09:08, 9 March 2017
Line 7:		Line 7:
	Description: Crystal structure of ASCH from Zymomonas mobilis		Description: Crystal structure of ASCH from Zymomonas mobilis
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kim, J.S]]
	[[Category: Park, S.Y]]		[[Category: Park, S.Y]]
	[[Category: Ha, S.C]]		[[Category: Ha, S.C]]
		+	[[Category: Kim, J.S]]

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

OCA — Fri, 09 Sep 2016 12:06:27 GMT

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

←Older revision

Revision as of 12:06, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5guq is ON HOLD Authors: Ha, S.C., Park, S.Y., Kim, J.S. Description: Crystal structure of ASCH from Zymomonas mobilis [[Category: Unreleased Struc...

OCA — Fri, 09 Sep 2016 12:06:25 GMT

New page: '''Unreleased structure''' The entry 5guq is ON HOLD Authors: Ha, S.C., Park, S.Y., Kim, J.S. Description: Crystal structure of ASCH from Zymomonas mobilis [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5guq is ON HOLD

Authors: Ha, S.C., Park, S.Y., Kim, J.S.

Description: Crystal structure of ASCH from Zymomonas mobilis
[[Category: Unreleased Structures]]
[[Category: Kim, J.S]]
[[Category: Park, S.Y]]
[[Category: Ha, S.C]]