7qod - Revision history

OCA at 07:53, 1 May 2024

2024-05-01T07:53:46Z

←Older revision		Revision as of 07:53, 1 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7qod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOD 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=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.85Å</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=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=7qod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qod OCA], [https://pdbe.org/7qod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qod RCSB], [https://www.ebi.ac.uk/pdbsum/7qod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qod 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=7qod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qod OCA], [https://pdbe.org/7qod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qod RCSB], [https://www.ebi.ac.uk/pdbsum/7qod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qod ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q8NQV9_CORGL Q8NQV9_CORGL]]	+	[https://www.uniprot.org/uniprot/Q8NQV9_CORGL Q8NQV9_CORGL]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The bacterial stringent response involves wide-ranging metabolic reprogramming aimed at increasing long-term survivability during stress conditions. One of the hallmarks of the stringent response is the production of a set of modified nucleotides, known as alarmones, which affect a multitude of cellular pathways in diverse ways. Production and degradation of these molecules depend on the activity of enzymes from the RelA/SpoT homologous (RSH) family, which come in both bifunctional (containing domains to both synthesize and hydrolyze alarmones) and monofunctional (consisting of only synthetase or hydrolase domain) variants, of which the structure, activity, and regulation of the bifunctional RSHs have been studied most intensely. Despite playing an important role in guanosine nucleotide homeostasis in particular, mechanisms of regulation of the small alarmone hydrolases (SAH) are still rather unclear. Here, we present crystal structures of SAH enzymes from Corynebacterium glutamicum (RelHCg) and Leptospira levettii (RelHLl) and show that while being highly similar, structural differences in substrate access and dimer conformations might be important for regulating their activity. We propose that a varied dimer form is a general property of the SAH family, based on current structural information as well as prediction models for this class of enzymes. Finally, subtle structural variations between monofunctional and bifunctional enzymes point to how these different classes of enzymes are regulated.	+
-		+
-	Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response.,Bisiak F, Chrenkova A, Zhang SD, Pedersen JN, Otzen DE, Zhang YE, Brodersen DE J Biol Chem. 2022 Jun 14:102142. doi: 10.1016/j.jbc.2022.102142. PMID:35714769<ref>PMID:35714769</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7qod" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:42, 8 September 2022

2022-09-08T04:42:13Z

←Older revision		Revision as of 04:42, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7qod' size='340' side='right'caption='[[7qod]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='7qod' size='340' side='right'caption='[[7qod]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7qod]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7qod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOD 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=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Guanosine-3',5'-bis(diphosphate)_3'-diphosphatase Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.7.2 3.1.7.2] </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=7qod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qod OCA], [https://pdbe.org/7qod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qod RCSB], [https://www.ebi.ac.uk/pdbsum/7qod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qod 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=7qod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qod OCA], [https://pdbe.org/7qod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qod RCSB], [https://www.ebi.ac.uk/pdbsum/7qod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qod ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q8NQV9_CORGL Q8NQV9_CORGL]]
	<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: Corynebacterium glutamicum ATCC 13032]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bisiak, F]]	+	[[Category: Bisiak F]]
-	[[Category: Brodersen~~, D E~~]]	+	[[Category: Brodersen DE]]
-	[[Category: Chrenkova, A]]	+	[[Category: Chrenkova A]]
-	~~[[Category: Alarmone]]~~	+
-	~~[[Category: Hd domain]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Stress response~~]]	+

OCA at 18:15, 27 July 2022

2022-07-27T18:15:52Z

←Older revision		Revision as of 18:15, 27 July 2022
Line 1:		Line 1:

	==Native structure of a small alarmone hydrolase (RelH) from Corynebacterium glutamicum==		==Native structure of a small alarmone hydrolase (RelH) from Corynebacterium glutamicum==
-	<StructureSection load='7qod' size='340' side='right'caption='[[7qod]]' scene=''>	+	<StructureSection load='7qod' size='340' side='right'caption='[[7qod]], [[Resolution\|resolution]] 1.85Å' 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=7QOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7qod]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOD 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=7qod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qod OCA], [https://pdbe.org/7qod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qod RCSB], [https://www.ebi.ac.uk/pdbsum/7qod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qod 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=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Guanosine-3',5'-bis(diphosphate)_3'-diphosphatase Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.7.2 3.1.7.2] </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=7qod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qod OCA], [https://pdbe.org/7qod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qod RCSB], [https://www.ebi.ac.uk/pdbsum/7qod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qod ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The bacterial stringent response involves wide-ranging metabolic reprogramming aimed at increasing long-term survivability during stress conditions. One of the hallmarks of the stringent response is the production of a set of modified nucleotides, known as alarmones, which affect a multitude of cellular pathways in diverse ways. Production and degradation of these molecules depend on the activity of enzymes from the RelA/SpoT homologous (RSH) family, which come in both bifunctional (containing domains to both synthesize and hydrolyze alarmones) and monofunctional (consisting of only synthetase or hydrolase domain) variants, of which the structure, activity, and regulation of the bifunctional RSHs have been studied most intensely. Despite playing an important role in guanosine nucleotide homeostasis in particular, mechanisms of regulation of the small alarmone hydrolases (SAH) are still rather unclear. Here, we present crystal structures of SAH enzymes from Corynebacterium glutamicum (RelHCg) and Leptospira levettii (RelHLl) and show that while being highly similar, structural differences in substrate access and dimer conformations might be important for regulating their activity. We propose that a varied dimer form is a general property of the SAH family, based on current structural information as well as prediction models for this class of enzymes. Finally, subtle structural variations between monofunctional and bifunctional enzymes point to how these different classes of enzymes are regulated.
		+
		+	Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response.,Bisiak F, Chrenkova A, Zhang SD, Pedersen JN, Otzen DE, Zhang YE, Brodersen DE J Biol Chem. 2022 Jun 14:102142. doi: 10.1016/j.jbc.2022.102142. PMID:35714769<ref>PMID:35714769</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7qod" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bisiak F]]	+	[[Category: Bisiak, F]]
-	[[Category: Brodersen DE]]	+	[[Category: Brodersen, D E]]
-	[[Category: Chrenkova A]]	+	[[Category: Chrenkova, A]]
		+	[[Category: Alarmone]]
		+	[[Category: Hd domain]]
		+	[[Category: Hydrolase]]
		+	[[Category: Stress response]]

OCA at 05:15, 13 July 2022

2022-07-13T05:15:22Z

←Older revision		Revision as of 05:15, 13 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7qod is ~~ON HOLD until Paper Publication~~	+	==Native structure of a small alarmone hydrolase (RelH) from Corynebacterium glutamicum==
-		+	<StructureSection load='7qod' size='340' side='right'caption='[[7qod]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QOD 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=7qod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qod OCA], [https://pdbe.org/7qod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qod RCSB], [https://www.ebi.ac.uk/pdbsum/7qod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qod ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bisiak F]]
		+	[[Category: Brodersen DE]]
		+	[[Category: Chrenkova A]]

OCA at 05:25, 2 February 2022

2022-02-02T05:25:20Z

←Older revision		Revision as of 05:25, 2 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2021-12-29T11:58:56Z

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

←Older revision

Revision as of 11:58, 29 December 2021

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

2021-12-29T11:58:55Z

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

New page

'''Unreleased structure'''

The entry 7qod is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]