7wik - Revision history

OCA at 17:41, 29 November 2023

2023-11-29T17:41:07Z

←Older revision		Revision as of 17:41, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7wik]] is a 4 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=7WIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WIK FirstGlance]. <br>		<table><tr><td colspan='2'>[[7wik]] is a 4 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=7WIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WIK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.87Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7wik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wik OCA], [https://pdbe.org/7wik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wik RCSB], [https://www.ebi.ac.uk/pdbsum/7wik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wik 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=7wik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wik OCA], [https://pdbe.org/7wik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wik RCSB], [https://www.ebi.ac.uk/pdbsum/7wik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wik ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7wik" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7wik" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:24, 21 December 2022

2022-12-21T09:24:01Z

←Older revision		Revision as of 09:24, 21 December 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7wik is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of oligoribonuclease of Mycobacterium smegmatis mc2 155==
		+	<StructureSection load='7wik' size='340' side='right'caption='[[7wik]], [[Resolution\|resolution]] 1.87Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7wik]] is a 4 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=7WIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WIK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7wik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wik OCA], [https://pdbe.org/7wik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wik RCSB], [https://www.ebi.ac.uk/pdbsum/7wik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wik ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0R1E6_MYCS2 A0R1E6_MYCS2] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Oligoribonucleases (Orns) are highly conserved DnaQ-fold 3'-5' exoribonucleases that have been found to carry out the last step of cyclic-di-GMP (c-di-GMP) degradation, that is, pGpG to GMP in several bacteria. Removal of pGpG is critical for c-di-GMP homeostasis, as excess uncleaved pGpG can have feedback inhibition on phosphodiesterases, thereby perturbing cellular signaling pathways regulated by c-di-GMP. Perturbation of c-di-GMP levels not only affects survival under hypoxic, reductive stress, or nutrient-limiting conditions but also affects pathogenicity in infection models as well as antibiotic response in mycobacteria. Here, we have determined the crystal structure of MSMEG_4724, the Orn of Mycobacterium smegmatis (Ms_orn) to 1.87 A resolution to investigate the function of its extended C-terminal tail that is unique among bacterial Orns. Ms_orn is a homodimer with the canonical RNase-H fold of exoribonucleases and conserved catalytic residues in the active site. Further examination of the substrate-binding site with a modeled pGpG emphasized the role of a phosphate cap and "3'OH cap" in constricting a 2-mer substrate in the active site. The unique C-terminal tail of Ms_orn aids dimerization by forming a handshake-like flap over the second protomer of the dimer. Our thermal and denaturant-induced unfolding experiments suggest that it helps in higher stability of Ms_orn as compared with Escherichia coli Orn or a C-terminal deletion mutant. We also show that the C-terminal tail is required for modulating response to stress agents in vivo. These results will help in further evaluating the role of signaling and regulation by c-di-GMP in mycobacteria.

-	~~Authors~~:	+	Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer.,Badhwar P, Khan SH, Taneja B J Biol Chem. 2022 Oct 14;298(12):102595. doi: 10.1016/j.jbc.2022.102595. PMID:36244449<ref>PMID:36244449</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7wik" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mycolicibacterium smegmatis MC2 155]]
		+	[[Category: Badhwar P]]
		+	[[Category: Taneja B]]

OCA at 05:42, 27 January 2022

2022-01-27T05:42:32Z

←Older revision		Revision as of 05:42, 27 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2022-01-12T08:46:19Z

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

←Older revision

Revision as of 08:46, 12 January 2022

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

2022-01-12T08:46:18Z

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

New page

'''Unreleased structure'''

The entry 7wik is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]