5o5s - Revision history

OCA at 19:09, 29 November 2023

OCA — Wed, 29 Nov 2023 19:09:03 GMT

←Older revision		Revision as of 19:09, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='5o5s' size='340' side='right'caption='[[5o5s]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='5o5s' size='340' side='right'caption='[[5o5s]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5O5S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O5S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 1.17Å</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=5o5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5s OCA], [~~http~~://pdbe.org/5o5s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o5s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o5s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5s ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=5o5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5s OCA], [https://pdbe.org/5o5s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o5s RCSB], [https://www.ebi.ac.uk/pdbsum/5o5s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RAPZ_ECOLI RAPZ_ECOLI]] Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ. When glucosamine-6-phosphate (GlcN6P) concentrations are high in the cell, RapZ binds GlmZ and targets it to cleavage by RNase E. Consequently, GlmZ is inactivated and unable to activate GlmS synthesis. Under low GlcN6P concentrations, RapZ is sequestered and inactivated by an other regulatory small RNA, GlmY, preventing GlmZ degradation and leading to synthesis of GlmS (PubMed:17824929, PubMed:23475961). Displays ATPase and GTPase activities in vitro. Can also hydrolyze pNPP (PubMed:19074378).<ref>PMID:17824929</ref> <ref>PMID:19074378</ref> <ref>PMID:23475961</ref>	+	[https://www.uniprot.org/uniprot/RAPZ_ECOLI RAPZ_ECOLI] Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ. When glucosamine-6-phosphate (GlcN6P) concentrations are high in the cell, RapZ binds GlmZ and targets it to cleavage by RNase E. Consequently, GlmZ is inactivated and unable to activate GlmS synthesis. Under low GlcN6P concentrations, RapZ is sequestered and inactivated by an other regulatory small RNA, GlmY, preventing GlmZ degradation and leading to synthesis of GlmS (PubMed:17824929, PubMed:23475961). Displays ATPase and GTPase activities in vitro. Can also hydrolyze pNPP (PubMed:19074378).<ref>PMID:17824929</ref> <ref>PMID:19074378</ref> <ref>PMID:23475961</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Durica-Mitic, S]]	+	[[Category: Durica-Mitic S]]
-	[[Category: Ficner, R]]	+	[[Category: Ficner R]]
-	[[Category: Gonzalez~~, G M~~]]	+	[[Category: Gonzalez GM]]
-	[[Category: Gorke, B]]	+	[[Category: Gorke B]]
-	[[Category: Hardwick~~, S W~~]]	+	[[Category: Hardwick SW]]
-	[[Category: Luisi~~, B F~~]]	+	[[Category: Luisi BF]]
-	[[Category: Moncrieffe, M]]	+	[[Category: Moncrieffe M]]
-	[[Category: Neumann, P]]	+	[[Category: Neumann P]]
-	[[Category: Resch, M]]	+	[[Category: Resch M]]
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Rna binding amino-sugar metabolism kinase like domain pfk like domain~~]]	+

OCA at 12:17, 26 August 2020

OCA — Wed, 26 Aug 2020 12:17:58 GMT

←Older revision		Revision as of 12:17, 26 August 2020
Line 1:		Line 1:

	==X-ray crystal structure of the RapZ C-terminal domain from Escherichia coli==		==X-ray crystal structure of the RapZ C-terminal domain from Escherichia coli==
-	<StructureSection load='5o5s' size='340' side='right' caption='[[5o5s]], [[Resolution\|resolution]] 1.17Å' scene=''>	+	<StructureSection load='5o5s' size='340' side='right'caption='[[5o5s]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5S OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O5S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5O5S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=5o5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5s OCA], [http://pdbe.org/5o5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5s RCSB], [http://www.ebi.ac.uk/pdbsum/5o5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5s 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=5o5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5s OCA], [http://pdbe.org/5o5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5s RCSB], [http://www.ebi.ac.uk/pdbsum/5o5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Durica-Mitic, S]]		[[Category: Durica-Mitic, S]]
	[[Category: Ficner, R]]		[[Category: Ficner, R]]

OCA at 06:59, 18 October 2017

OCA — Wed, 18 Oct 2017 06:59:53 GMT

←Older revision		Revision as of 06:59, 18 October 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RAPZ_ECOLI RAPZ_ECOLI]] Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ. When glucosamine-6-phosphate (GlcN6P) concentrations are high in the cell, RapZ binds GlmZ and targets it to cleavage by RNase E. Consequently, GlmZ is inactivated and unable to activate GlmS synthesis. Under low GlcN6P concentrations, RapZ is sequestered and inactivated by an other regulatory small RNA, GlmY, preventing GlmZ degradation and leading to synthesis of GlmS (PubMed:17824929, PubMed:23475961). Displays ATPase and GTPase activities in vitro. Can also hydrolyze pNPP (PubMed:19074378).<ref>PMID:17824929</ref> <ref>PMID:19074378</ref> <ref>PMID:23475961</ref>		[[http://www.uniprot.org/uniprot/RAPZ_ECOLI RAPZ_ECOLI]] Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ. When glucosamine-6-phosphate (GlcN6P) concentrations are high in the cell, RapZ binds GlmZ and targets it to cleavage by RNase E. Consequently, GlmZ is inactivated and unable to activate GlmS synthesis. Under low GlcN6P concentrations, RapZ is sequestered and inactivated by an other regulatory small RNA, GlmY, preventing GlmZ degradation and leading to synthesis of GlmS (PubMed:17824929, PubMed:23475961). Displays ATPase and GTPase activities in vitro. Can also hydrolyze pNPP (PubMed:19074378).<ref>PMID:17824929</ref> <ref>PMID:19074378</ref> <ref>PMID:23475961</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In phylogenetically diverse bacteria, the conserved protein RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. RapZ contributes to the control of glucosamine phosphate biogenesis by selectively presenting the regulatory small RNA GlmZ to the essential ribonuclease RNase E for inactivation. Here, we report the crystal structures of full length Escherichia coli RapZ at 3.40 A and 3.25 A, and its isolated C-terminal domain at 1.17 A resolution. The structural data confirm that the N-terminal domain of RapZ possesses a kinase fold, whereas the C-terminal domain bears closest homology to a subdomain of 6-phosphofructokinase, an important enzyme in the glycolytic pathway. RapZ self-associates into a domain swapped dimer of dimers, and in vivo data support the importance of quaternary structure in RNA-mediated regulation of target gene expression. Based on biochemical, structural and genetic data, we suggest a mechanism for binding and presentation by RapZ of GlmZ and the closely related decoy sRNA, GlmY. We discuss a scenario for the molecular evolution of RapZ through re-purpose of enzyme components from central metabolism.
		+
		+	Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.,Gonzalez GM, Durica-Mitic S, Hardwick SW, Moncrieffe MC, Resch M, Neumann P, Ficner R, Gorke B, Luisi BF Nucleic Acids Res. 2017 Sep 5. doi: 10.1093/nar/gkx732. PMID:28977623<ref>PMID:28977623</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5o5s" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA: Protected "5o5s" [edit=sysop:move=sysop]

OCA — Tue, 05 Sep 2017 14:55:09 GMT

Protected "5o5s" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:55, 5 September 2017

OCA: New page: ==X-ray crystal structure of the RapZ C-terminal domain from Escherichia coli== == Structural highlights ==
<table><tr><td colspan='2'>[[5o5s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5S FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=5o5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5s OCA], [http://pdbe.org/5o5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5s RCSB], [http://www.ebi.ac.uk/pdbsum/5o5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5s ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/RAPZ_ECOLI RAPZ_ECOLI]] Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ. When glucosamine-6-phosphate (GlcN6P) concentrations are high in the cell, RapZ binds GlmZ and targets it to cleavage by RNase E. Consequently, GlmZ is inactivated and unable to activate GlmS synthesis. Under low GlcN6P concentrations, RapZ is sequestered and inactivated by an other regulatory small RNA, GlmY, preventing GlmZ degradation and leading to synthesis of GlmS (PubMed:17824929, PubMed:23475961). Displays ATPase and GTPase activities in vitro. Can also hydrolyze pNPP (PubMed:19074378).<ref>PMID:17824929</ref> <ref>PMID:19074378</ref> <ref>PMID:23475961</ref>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Durica-Mitic, S]]
[[Category: Ficner, R]]
[[Category: Gonzalez, G M]]
[[Category: Gorke, B]]
[[Category: Hardwick, S W]]
[[Category: Luisi, B F]]
[[Category: Moncrieffe, M]]
[[Category: Neumann, P]]
[[Category: Resch, M]]
[[Category: Chaperone]]
[[Category: Rna binding amino-sugar metabolism kinase like domain pfk like domain]]