5yrp - Revision history

OCA at 08:36, 22 November 2023

OCA — Wed, 22 Nov 2023 08:36:09 GMT

←Older revision		Revision as of 08:36, 22 November 2023
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	<StructureSection load='5yrp' size='340' side='right'caption='[[5yrp]], [[Resolution\|resolution]] 2.99Å' scene=''>		<StructureSection load='5yrp' size='340' side='right'caption='[[5yrp]], [[Resolution\|resolution]] 2.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YRP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YRP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.99Å</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=MG:MAGNESIUM+ION'>MG</scene>, <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~~://proteopedia.org/fgij/fg.htm?mol=5yrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrp OCA], [~~http~~://pdbe.org/5yrp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yrp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yrp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrp 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=5yrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrp OCA], [https://pdbe.org/5yrp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yrp RCSB], [https://www.ebi.ac.uk/pdbsum/5yrp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0QUG3_MYCS2 A0QUG3_MYCS2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, H J~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: Chen, Y]]	+	[[Category: Chen HJ]]
-	[[Category: Jiang~~, Y L~~]]	+	[[Category: Chen Y]]
-	[[Category: Li, Q]]	+	[[Category: Jiang YL]]
-	[[Category: Luo, Y]]	+	[[Category: Li Q]]
-	[[Category: Zhou~~, C Z~~]]	+	[[Category: Luo Y]]
-	[[Category: Li, N]]	+	[[Category: Zhou CZ]]
-	~~[[Category: Biosynthetic protein]]~~	+	[[Category: Li N]]
-	~~[[Category: C-di-gmp]]~~	+
-	~~[[Category: Diguanylate cyclase]]~~	+
-	~~[[Category: Gaf]]~~	+
-	~~[[Category: Phosphodiesterase~~]]	+

OCA at 09:26, 21 October 2020

OCA — Wed, 21 Oct 2020 09:26:25 GMT

←Older revision		Revision as of 09:26, 21 October 2020
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	==Crystal structure of the EAL domain of Mycobacterium smegmatis DcpA==		==Crystal structure of the EAL domain of Mycobacterium smegmatis DcpA==
-	<StructureSection load='5yrp' size='340' side='right' caption='[[5yrp]], [[Resolution\|resolution]] 2.99Å' scene=''>	+	<StructureSection load='5yrp' size='340' side='right'caption='[[5yrp]], [[Resolution\|resolution]] 2.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YRP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YRP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5yrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrp OCA], [http://pdbe.org/5yrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrp RCSB], [http://www.ebi.ac.uk/pdbsum/5yrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrp 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=5yrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrp OCA], [http://pdbe.org/5yrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrp RCSB], [http://www.ebi.ac.uk/pdbsum/5yrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrp 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: Large Structures]]
	[[Category: Chen, H J]]		[[Category: Chen, H J]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]

OCA at 06:14, 9 May 2018

OCA — Wed, 09 May 2018 06:14:15 GMT

←Older revision		Revision as of 06:14, 9 May 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yrp is ~~ON HOLD~~	+	==Crystal structure of the EAL domain of Mycobacterium smegmatis DcpA==
		+	<StructureSection load='5yrp' size='340' side='right' caption='[[5yrp]], [[Resolution\|resolution]] 2.99Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yrp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YRP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5yrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrp OCA], [http://pdbe.org/5yrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrp RCSB], [http://www.ebi.ac.uk/pdbsum/5yrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrp ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The second messenger c-di-GMP [bis-(3'-5')-cyclic dimeric guanosine monophosphate] plays a key role in bacterial growth, survival and pathogenesis, and thus its intracellular homeostasis should be finely maintained. Mycobacterium smegmatis encodes a GAF (mammalian cGMP-regulated phosphodiesterases, Anabaenaadenylyl cyclases and Escherichia coli transcription activator FhlA) domain containing bifunctional enzyme DcpA (diguanylate cyclase and phosphodiesterase A) that catalyzes the synthesis and hydrolysis of c-di-GMP. Here, we found that M. smegmatis DcpA catalyzes the hydrolysis of c-di-GMP at a higher velocity, compared with synthetic activity, resulting in a sum reaction from the ultimate substrate GTP to the final product pGpG [5'-phosphoguanylyl-(3'-5')-guanosine]. Fusion with the N-terminal GAF domain enables the GGDEF (Gly-Gly-Asp-Glu-Phe) domain of DcpA to dimerize and accordingly gain synthetic activity. Screening of putative metabolites revealed that GDP is the ligand of the GAF domain. Binding of GDP to the GAF domain down-regulates synthetic activity, but up-regulates hydrolytic activity, which, in consequence, might enable a timely response to the transient accumulation of c-di-GMP at the stationary phase or under stresses. Combined with the crystal structure of the EAL (Glu-Ala-Leu) domain and the small-angle X-ray scattering data, we propose a putative regulatory model of the GAF domain finely tuned by the intracellular GTP/GDP ratio. These findings help us to better understand the concerted control of the synthesis and hydrolysis of c-di-GMP in M. smegmatis in various microenvironments.

-	~~Authors~~:	+	The GDP-switched GAF domain of DcpA modulates the concerted synthesis/hydrolysis of c-di-GMP in Mycobacterium smegmatis.,Chen HJ, Li N, Luo Y, Jiang YL, Zhou CZ, Chen Y, Li Q Biochem J. 2018 Apr 9;475(7):1295-1308. doi: 10.1042/BCJ20180079. PMID:29555845<ref>PMID:29555845</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yrp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, H J]]
		+	[[Category: Chen, Y]]
		+	[[Category: Jiang, Y L]]
		+	[[Category: Li, Q]]
		+	[[Category: Luo, Y]]
		+	[[Category: Zhou, C Z]]
		+	[[Category: Li, N]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: C-di-gmp]]
		+	[[Category: Diguanylate cyclase]]
		+	[[Category: Gaf]]
		+	[[Category: Phosphodiesterase]]

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

OCA — Wed, 15 Nov 2017 06:18:16 GMT

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

←Older revision

Revision as of 06:18, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yrp is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Nov 2017 06:18:15 GMT

New page: '''Unreleased structure''' The entry 5yrp is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yrp is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]