4o1h - Revision history

OCA at 08:51, 18 January 2023

OCA — Wed, 18 Jan 2023 08:51:29 GMT

←Older revision		Revision as of 08:51, 18 January 2023
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	==Crystal Structure of the regulatory domain of AmeGlnR==		==Crystal Structure of the regulatory domain of AmeGlnR==
-	<StructureSection load='4o1h' size='340' side='right' caption='[[4o1h]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='4o1h' size='340' side='right'caption='[[4o1h]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o1h]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_mediterranei"_margalith_and_beretta_1960 "streptomyces~~ mediterranei~~" margalith and beretta 1960~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O1H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4O1H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o1h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_mediterranei Amycolatopsis mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O1H FirstGlance]. <br>
-	</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>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o1i\|4o1i]]</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=4o1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o1h OCA], [https://pdbe.org/4o1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o1h RCSB], [https://www.ebi.ac.uk/pdbsum/4o1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o1h ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GlnR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</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=4o1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o1h OCA], [~~http~~://pdbe.org/4o1h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4o1h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4o1h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4o1h ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8GD11_AMYMD Q8GD11_AMYMD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptomyces~~ mediterranei ~~margalith and beretta 1960~~]]	+	[[Category: Amycolatopsis mediterranei]]
-	[[Category: ~~Lin, W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Wang, C~~]]	+	[[Category: Lin W]]
-	[[Category: ~~Zhang, P~~]]	+	[[Category: Wang C]]
-	[[Category: ~~Homodimeric receiver domain]]~~	+	[[Category: Zhang P]]
-	~~[[Category: Transcription regulator~~]]	+

OCA at 07:56, 11 August 2016

OCA — Thu, 11 Aug 2016 07:56:11 GMT

←Older revision		Revision as of 07:56, 11 August 2016
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		+
	==Crystal Structure of the regulatory domain of AmeGlnR==		==Crystal Structure of the regulatory domain of AmeGlnR==
	<StructureSection load='4o1h' size='340' side='right' caption='[[4o1h]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='4o1h' size='340' side='right' caption='[[4o1h]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o1i\|4o1i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o1i\|4o1i]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GlnR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GlnR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</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=4o1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o1h RCSB], [http://www.ebi.ac.uk/pdbsum/4o1h PDBsum]</span></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=4o1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o1h OCA], [http://pdbe.org/4o1h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o1h RCSB], [http://www.ebi.ac.uk/pdbsum/4o1h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o1h ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4o1h" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:02, 5 January 2015

OCA — Mon, 05 Jan 2015 09:02:58 GMT

←Older revision		Revision as of 09:02, 5 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o1h]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_mediterranei"_margalith_and_beretta_1960 "streptomyces mediterranei" margalith and beretta 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O1H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O1H FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o1h]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_mediterranei"_margalith_and_beretta_1960 "streptomyces mediterranei" margalith and beretta 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O1H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O1H FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o1i\|4o1i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o1i\|4o1i]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GlnR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GlnR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4o1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o1h RCSB], [http://www.ebi.ac.uk/pdbsum/4o1h PDBsum]</span></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=4o1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o1h RCSB], [http://www.ebi.ac.uk/pdbsum/4o1h PDBsum]</span></td></tr>
-	<table>	+	</table>
	<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: Streptomyces mediterranei margalith and beretta 1960]]		[[Category: Streptomyces mediterranei margalith and beretta 1960]]
-	[[Category: Lin, W.]]	+	[[Category: Lin, W]]
-	[[Category: Wang, C.]]	+	[[Category: Wang, C]]
-	[[Category: Zhang, P.]]	+	[[Category: Zhang, P]]
	[[Category: Homodimeric receiver domain]]		[[Category: Homodimeric receiver domain]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]

OCA at 05:21, 18 June 2014

OCA — Wed, 18 Jun 2014 05:21:37 GMT

←Older revision		Revision as of 05:21, 18 June 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4o1h\| PDB=4o1h \| SCENE= }}~~	+	==Crystal Structure of the regulatory domain of AmeGlnR==
-	===Crystal Structure of the regulatory domain of AmeGlnR===	+	<StructureSection load='4o1h' size='340' side='right' caption='[[4o1h]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4o1h]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_mediterranei"_margalith_and_beretta_1960 "streptomyces mediterranei" margalith and beretta 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O1H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O1H FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o1i\|4o1i]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GlnR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4o1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o1h RCSB], [http://www.ebi.ac.uk/pdbsum/4o1h PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The OmpR/PhoB subfamily protein GlnR of actinomycetes is an orphan response regulator that globally coordinates the expression of genes related to nitrogen metabolism. Biochemical and genetic analyses reveal that the functional GlnR from Amycolatopsis mediterranei is unphosphorylated at the potential phosphorylation Asp50 residue in the N-terminal receiver domain. The crystal structure of this receiver domain demonstrates that it forms a homodimer through the alpha4-beta5-alpha5 dimer interface highly similar to the phosphorylated typical response regulator, whereas the so-called "phosphorylation pocket" is not conserved, with its space being occupied by an Arg52 from the beta3-alpha3 loop. Both in vitro and in vivo experiments confirm that GlnR forms a functional homodimer via its receiver domain and suggest that the charge interactions of Asp50 with the highly conserved Arg52 and Thr9 in the receiver domain may be crucial in maintaining the proper conformation for homodimerization, as also supported by molecular dynamics simulations of the wild type GlnR versus the deficient mutant GlnR(D50A). This model is backed by the distinct phenotypes of the total deficient GlnR(R52A/T9A) double mutant versus the single mutants of GlnR (i.e. D50N, D50E, R52A and T9A), which have only minor effects upon both dimerization and physiological function of GlnR in vivo, albeit their DNA binding ability is weakened compared with that of the wild type. By integrating the supportive data of GlnRs from the model Streptomyces coelicolor and the pathogenic Mycobacterium tuberculosis, we conclude that the actinomycete GlnR is atypical with respect to its unphosphorylated conserved Asp residue being involved in the critical Arg/Asp/Thr charge interactions, which is essential for maintaining the biologically active homodimer conformation.

-	~~==About this Structure==~~	+	Atypical OmpR/PhoB Subfamily Response Regulator GlnR of Actinomycetes Functions as a Homodimer, Stabilized by the Unphosphorylated Conserved Asp-focused Charge Interactions.,Lin W, Wang Y, Han X, Zhang Z, Wang C, Wang J, Yang H, Lu Y, Jiang W, Zhao GP, Zhang P J Biol Chem. 2014 May 30;289(22):15413-15425. Epub 2014 Apr 14. PMID:24733389<ref>PMID:24733389</ref>
-	~~[[4o1h]] is~~ a ~~4 chain structure~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.~~il/oca-bin~~/~~ocashort?id~~=~~4O1H OCA~~].	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Streptomyces mediterranei margalith and beretta 1960]]
	[[Category: Lin, W.]]		[[Category: Lin, W.]]
	[[Category: Wang, C.]]		[[Category: Wang, C.]]

OCA at 07:57, 23 April 2014

OCA — Wed, 23 Apr 2014 07:57:48 GMT

←Older revision		Revision as of 07:57, 23 April 2014
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4o1h\| PDB=4o1h \| SCENE= }}
		+	===Crystal Structure of the regulatory domain of AmeGlnR===

-	~~The entry~~ 4o1h is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4o1h]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O1H OCA].
-	~~Authors~~: Lin, W., Wang, C., Zhang, P.	+	[[Category: Lin, W.]]
-		+	[[Category: Wang, C.]]
-	~~Description~~: ~~Crystal Structure of the regulatory~~ domain ~~of AmeGlnR~~	+	[[Category: Zhang, P.]]
		+	[[Category: Homodimeric receiver domain]]
		+	[[Category: Transcription regulator]]

OCA at 07:18, 19 March 2014

OCA — Wed, 19 Mar 2014 07:18:01 GMT

←Older revision		Revision as of 07:18, 19 March 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4o1h is ON HOLD	+	The entry 4o1h is ON HOLD until Paper Publication

	Authors: Lin, W., Wang, C., Zhang, P.		Authors: Lin, W., Wang, C., Zhang, P.

	Description: Crystal Structure of the regulatory domain of AmeGlnR		Description: Crystal Structure of the regulatory domain of AmeGlnR

OCA at 09:21, 8 January 2014

OCA — Wed, 08 Jan 2014 09:21:57 GMT

←Older revision		Revision as of 09:21, 8 January 2014
Line 3:		Line 3:
	The entry 4o1h is ON HOLD		The entry 4o1h is ON HOLD

-	Authors: Lin, ~~Wei~~, Wang,~~Chengyuan~~, Zhang, ~~Peng~~	+	Authors: Lin, W., Wang, C., Zhang, P.

	Description: Crystal Structure of the regulatory domain of AmeGlnR		Description: Crystal Structure of the regulatory domain of AmeGlnR

OCA: Protected "4o1h" [edit=sysop:move=sysop]

OCA — Wed, 25 Dec 2013 09:30:18 GMT

Protected "4o1h" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:30, 25 December 2013

OCA: New page: '''Unreleased structure''' The entry 4o1h is ON HOLD Authors: Lin, Wei, Wang,Chengyuan, Zhang, Peng Description: Crystal Structure of the regulatory domain of AmeGlnR

OCA — Wed, 25 Dec 2013 09:30:16 GMT

New page: '''Unreleased structure''' The entry 4o1h is ON HOLD Authors: Lin, Wei, Wang,Chengyuan, Zhang, Peng Description: Crystal Structure of the regulatory domain of AmeGlnR

New page

'''Unreleased structure'''

The entry 4o1h is ON HOLD

Authors: Lin, Wei, Wang,Chengyuan, Zhang, Peng

Description: Crystal Structure of the regulatory domain of AmeGlnR