7tu0 - Revision history

OCA at 17:07, 18 October 2023

2023-10-18T17:07:52Z

←Older revision		Revision as of 17:07, 18 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7tu0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Leeuwenhoekiella_blandensis_MED217 Leeuwenhoekiella blandensis MED217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TU0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7tu0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Leeuwenhoekiella_blandensis_MED217 Leeuwenhoekiella blandensis MED217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TU0 FirstGlance]. <br>
-	</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=SO4:SULFATE+ION'>SO4</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]] 2.04Å</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=SO4:SULFATE+ION'>SO4</scene></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=7tu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tu0 OCA], [https://pdbe.org/7tu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7tu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tu0 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=7tu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tu0 OCA], [https://pdbe.org/7tu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7tu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tu0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A3XHN1_LEEBM A3XHN1_LEEBM]]	+	[https://www.uniprot.org/uniprot/A3XHN1_LEEBM A3XHN1_LEEBM]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:30, 8 September 2022

2022-09-08T05:30:05Z

←Older revision		Revision as of 05:30, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7tu0' size='340' side='right'caption='[[7tu0]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='7tu0' size='340' side='right'caption='[[7tu0]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7tu0]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TU0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tu0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Leeuwenhoekiella_blandensis_MED217 Leeuwenhoekiella blandensis MED217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TU0 FirstGlance]. <br>
	</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=SO4:SULFATE+ION'>SO4</scene></td></tr>		</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=SO4:SULFATE+ION'>SO4</scene></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=7tu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tu0 OCA], [https://pdbe.org/7tu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7tu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tu0 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=7tu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tu0 OCA], [https://pdbe.org/7tu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7tu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tu0 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/A3XHN1_LEEBM A3XHN1_LEEBM]]
-	Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human SAMHD1, a tetrameric dNTPase, and the hexameric E. coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 A) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 A) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.	+
-		+
-	High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP.,Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM J Biol Chem. 2022 May 25:~~102073. doi: 10.1016~~/~~j.jbc.2022.102073. PMID:35643313<ref>PMID:35643313<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7tu0" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hall, T M.T~~]]	+	[[Category: Leeuwenhoekiella blandensis MED217]]
-	[[Category: ~~Horng, J C~~]]	+	[[Category: Hall TMT]]
-	[[Category: ~~Klemm, B P~~]]	+	[[Category: Horng JC]]
-	[[Category: ~~Sikkema, A P~~]]	+	[[Category: Klemm BP]]
-	[[Category: ~~Dgtpase]]~~	+	[[Category: Sikkema AP]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nucleotide binding~~]]	+

OCA at 07:14, 20 July 2022

2022-07-20T07:14:04Z

←Older revision		Revision as of 07:14, 20 July 2022
Line 1:		Line 1:

	==Structure of the L. blandensis dGTPase bound to Mn==		==Structure of the L. blandensis dGTPase bound to Mn==
-	<StructureSection load='7tu0' size='340' side='right'caption='[[7tu0]]' scene=''>	+	<StructureSection load='7tu0' size='340' side='right'caption='[[7tu0]], [[Resolution\|resolution]] 2.04Å' 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=7TU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TU0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tu0]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TU0 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=7tu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tu0 OCA], [https://pdbe.org/7tu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7tu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tu0 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=7tu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tu0 OCA], [https://pdbe.org/7tu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7tu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tu0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human SAMHD1, a tetrameric dNTPase, and the hexameric E. coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 A) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 A) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.
		+
		+	High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP.,Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM J Biol Chem. 2022 May 25:102073. doi: 10.1016/j.jbc.2022.102073. PMID:35643313<ref>PMID:35643313</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7tu0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hall ~~TMT~~]]	+	[[Category: Hall, T M.T]]
-	[[Category: Horng JC]]	+	[[Category: Horng, J C]]
-	[[Category: Klemm BP]]	+	[[Category: Klemm, B P]]
-	[[Category: Sikkema AP]]	+	[[Category: Sikkema, A P]]
		+	[[Category: Dgtpase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nucleotide binding]]

OCA at 16:25, 6 July 2022

2022-07-06T16:25:12Z

←Older revision		Revision as of 16:25, 6 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7tu0 is ~~ON HOLD until Paper Publication~~	+	==Structure of the L. blandensis dGTPase bound to Mn==
-		+	<StructureSection load='7tu0' size='340' side='right'caption='[[7tu0]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TU0 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=7tu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tu0 OCA], [https://pdbe.org/7tu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7tu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tu0 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hall TMT]]
		+	[[Category: Horng JC]]
		+	[[Category: Klemm BP]]
		+	[[Category: Sikkema AP]]

OCA at 06:31, 23 February 2022

2022-02-23T06:31:19Z

←Older revision		Revision as of 06:31, 23 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7tu0 is ON HOLD	+	The entry 7tu0 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7tu0" [edit=sysop:move=sysop]

2022-02-09T06:21:54Z

Protected "7tu0" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:21, 9 February 2022

OCA: New page: '''Unreleased structure''' The entry 7tu0 is ON HOLD Authors: Description: Category: Unreleased Structures

2022-02-09T06:21:53Z

New page: '''Unreleased structure''' The entry 7tu0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7tu0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]