5ihy - Revision history

OCA at 13:53, 30 August 2023

OCA — Wed, 30 Aug 2023 13:53:34 GMT

←Older revision		Revision as of 13:53, 30 August 2023
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	<StructureSection load='5ihy' size='340' side='right'caption='[[5ihy]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5ihy' size='340' side='right'caption='[[5ihy]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ihy]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IHY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IHY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ihy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IHY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BIS30_00575 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])~~</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=5ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ihy OCA], [https://pdbe.org/5ihy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ihy RCSB], [https://www.ebi.ac.uk/pdbsum/5ihy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ihy 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=5ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ihy OCA], [~~http~~://pdbe.org/5ihy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ihy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ihy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ihy ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jeon~~, Y J~~]]	+	[[Category: Jeon YJ]]
-	[[Category: Song~~, W S~~]]	+	[[Category: Song WS]]
-	[[Category: Yoon~~, S I]]~~	+	[[Category: Yoon SI]]
-	~~[[Category: Hd domain]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:19, 3 June 2020

OCA — Wed, 03 Jun 2020 07:19:05 GMT

←Older revision		Revision as of 07:19, 3 June 2020
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	==The crystal structure of Bacillus subtilis SeMet-YpgQ==		==The crystal structure of Bacillus subtilis SeMet-YpgQ==
-	<StructureSection load='5ihy' size='340' side='right' caption='[[5ihy]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5ihy' size='340' side='right'caption='[[5ihy]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ihy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IHY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IHY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ihy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IHY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IHY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ihy OCA], [http://pdbe.org/5ihy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ihy RCSB], [http://www.ebi.ac.uk/pdbsum/5ihy PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BIS30_00575 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=5ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ihy OCA], [http://pdbe.org/5ihy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ihy RCSB], [http://www.ebi.ac.uk/pdbsum/5ihy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ihy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Jeon, Y J]]		[[Category: Jeon, Y J]]
	[[Category: Song, W S]]		[[Category: Song, W S]]

OCA at 12:08, 13 May 2016

OCA — Fri, 13 May 2016 12:08:07 GMT

←Older revision		Revision as of 12:08, 13 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5ihy is ~~ON HOLD~~	+	==The crystal structure of Bacillus subtilis SeMet-YpgQ==
		+	<StructureSection load='5ihy' size='340' side='right' caption='[[5ihy]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ihy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IHY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ihy OCA], [http://pdbe.org/5ihy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ihy RCSB], [http://www.ebi.ac.uk/pdbsum/5ihy PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The optimal balance of cellular nucleotides and the efficient elimination of non-canonical nucleotides are critical to avoiding erroneous mutation during DNA replication. One such mechanism involves the degradation of excessive or abnormal nucleotides by nucleotide-hydrolyzing enzymes. YpgQ contains the histidine-aspartate (HD) domain that is involved in the hydrolysis of nucleotides or nucleic acids, but the enzymatic activity and substrate specificity of YpgQ have never been characterized. Here, we unravel the catalytic activity and structural features of YpgQ to report the first Mn2+-dependent pyrophosphohydrolase that hydrolyzes (deoxy)ribonucleoside triphosphate [(d)NTP] to (deoxy)ribonucleoside monophosphate and pyrophosphate using the HD domain. YpgQ from Bacillus subtilis (bsYpgQ) displays a helical structure and assembles into a unique dimeric architecture that has not been observed in other HD domain-containing proteins. Each bsYpgQ monomer accommodates a metal ion and a nucleotide substrate in a cavity located between the N- and C-terminal lobes. The metal cofactor is coordinated by the canonical residues of the HD domain, namely, two histidine residues and two aspartate residues, and is positioned in close proximity to the beta-phosphate group of the nucleotide, allowing us to propose a nucleophilic attack mechanism for the nucleotide hydrolysis reaction. YpgQ enzymes from other bacterial species also catalyze pyrophosphohydrolysis but exhibit different substrate specificity. Comparative structural and mutational studies demonstrated that residues outside the major substrate-binding site of bsYpgQ are responsible for the species-specific substrate preference. Taken together, our structural and biochemical analyses highlight the substrate-recognition mode and catalysis mechanism of YpgQ in pyrophosphohydrolysis.

-	~~Authors:~~ Jeon, ~~Y.J.~~, Song, W.S., ~~Yoon, S~~.I.	+	Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase.,Jeon YJ, Park SC, Song WS, Kim OH, Oh BC, Yoon SI J Struct Biol. 2016 Apr 7. pii: S1047-8477(16)30061-2. doi:, 10.1016/j.jsb.2016.04.002. PMID:27062940<ref>PMID:27062940</ref>

-	~~Description: The crystal structure~~ of ~~Bacillus subtilis SeMet~~-~~YpgQ~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Jeon~~, ~~Y.J~~]]	+	<div class="pdbe-citations 5ihy" style="background-color:#fffaf0;"></div>
-	[[Category: Yoon, S.I]]	+	== References ==
-	[[Category: ~~Song, W.S~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Jeon, Y J]]
		+	[[Category: Song, W S]]
		+	[[Category: Yoon, S I]]
		+	[[Category: Hd domain]]
		+	[[Category: Hydrolase]]

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

OCA — Thu, 10 Mar 2016 02:21:23 GMT

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

←Older revision

Revision as of 02:21, 10 March 2016

OCA: New page: '''Unreleased structure''' The entry 5ihy is ON HOLD Authors: Jeon, Y.J., Song, W.S., Yoon, S.I. Description: The crystal structure of Bacillus subtilis SeMet-YpgQ [[Category: Unreleas...

OCA — Thu, 10 Mar 2016 02:21:22 GMT

New page: '''Unreleased structure''' The entry 5ihy is ON HOLD Authors: Jeon, Y.J., Song, W.S., Yoon, S.I. Description: The crystal structure of Bacillus subtilis SeMet-YpgQ [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5ihy is ON HOLD

Authors: Jeon, Y.J., Song, W.S., Yoon, S.I.

Description: The crystal structure of Bacillus subtilis SeMet-YpgQ
[[Category: Unreleased Structures]]
[[Category: Jeon, Y.J]]
[[Category: Yoon, S.I]]
[[Category: Song, W.S]]