5xaz - Revision history

OCA at 10:17, 27 March 2024

2024-03-27T10:17:49Z

←Older revision		Revision as of 10:17, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xaz' size='340' side='right'caption='[[5xaz]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5xaz' size='340' side='right'caption='[[5xaz]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xaz]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XAZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xaz]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_fradiae Streptomyces fradiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XAZ FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~5xay~~\|~~5xay~~]]</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]] 2.3Å</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=5xaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xaz OCA], [~~http~~://pdbe.org/5xaz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xaz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xaz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xaz 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=5xaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xaz OCA], [https://pdbe.org/5xaz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xaz RCSB], [https://www.ebi.ac.uk/pdbsum/5xaz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xaz ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9XCC7_STRFR Q9XCC7_STRFR]
-	Tetracycline Repressors (TetRs) modulate multi-drug efflux pathways in several pathogenic bacteria. In Streptomyces, they additionally regulate secondary metabolic pathways like antibiotic production. For instance, in the antibiotic producer Streptomyces fradiae, a layered network of TetRs regulate the levels of commercially important antibiotic tylosin, with TylP occupying the top of this cascading network. TetRs exist in two functional states; the DNA-bound and the ligand-bound form, which are allosterically regulated. Here, to develop deeper insights into the factors that govern allostery, the crystal structure of TylP was solved to a resolution of 2.3 A. The structure reveals that TylP possesses several unique features; notably, it harbors an unique C-terminal helix-loop extension that spans the entire length of the structure. This anchor connects the DNA binding domain (DBD) with the ligand binding domain (LBD) via a mix of positively charged and hydrogen-bonding interactions. Supporting EMSA studies with a series of DeltaC truncated versions show that a systematic deletion of this region results in complete loss of DNA binding. The structure additionally reveals that TylP is markedly different in the orientation of its DBD, LBD architecture and the dimeric geometry, from its hypothesized Streptomyces homologue CprB, which is a gamma- butyrolactone regulator. Rather, TylP is closer in structural design to macrolide binding TetRs, found in pathogens. Supporting MD studies suggest that TylP binds a macrolide intermediate in the tylosin pathway. Collectively, the structure along with corroborating biochemical studies provides insights into the novel mode of regulation of TetRs in antibiotic producing organisms.	+
-		+
-	Functional Insights into the Mode of DNA and Ligand Binding of the TetR Family Regulator TylP from Streptomyces fradiae.,Ray S, Maitra A, Biswas A, Panjikar S, Mondal J, Anand R J Biol Chem. 2017 Jul 24. pii: ~~jbc.M117.788000. doi: 10.1074~~/~~jbc.M117.788000. PMID:28739805<ref>PMID:28739805<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5xaz" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Anand, R~~]]	+	[[Category: Streptomyces fradiae]]
-	[[Category: ~~Panjikar, S~~]]	+	[[Category: Anand R]]
-	[[Category: ~~Ray,~~ S]]	+	[[Category: Panjikar S]]
-	[[Category: ~~Antibiotic regulation]]~~	+	[[Category: Ray S]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Hth dna binding domain]]~~	+
-	~~[[Category: Tetr family]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 07:31, 7 October 2020

2020-10-07T07:31:04Z

←Older revision		Revision as of 07:31, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of full length native tylp, a tetr regulator from streptomyces fradiae==		==Crystal structure of full length native tylp, a tetr regulator from streptomyces fradiae==
-	<StructureSection load='5xaz' size='340' side='right' caption='[[5xaz]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5xaz' size='340' side='right'caption='[[5xaz]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xaz]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XAZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xaz]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XAZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xay\|5xay]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xay\|5xay]]</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=5xaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xaz OCA], [http://pdbe.org/5xaz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xaz RCSB], [http://www.ebi.ac.uk/pdbsum/5xaz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xaz 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=5xaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xaz OCA], [http://pdbe.org/5xaz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xaz RCSB], [http://www.ebi.ac.uk/pdbsum/5xaz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xaz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Anand, R]]		[[Category: Anand, R]]
	[[Category: Panjikar, S]]		[[Category: Panjikar, S]]

OCA at 09:14, 9 August 2017

2017-08-09T09:14:25Z

←Older revision		Revision as of 09:14, 9 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xaz is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of full length native tylp, a tetr regulator from streptomyces fradiae==
		+	<StructureSection load='5xaz' size='340' side='right' caption='[[5xaz]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xaz]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XAZ FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xay\|5xay]]</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=5xaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xaz OCA], [http://pdbe.org/5xaz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xaz RCSB], [http://www.ebi.ac.uk/pdbsum/5xaz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xaz ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tetracycline Repressors (TetRs) modulate multi-drug efflux pathways in several pathogenic bacteria. In Streptomyces, they additionally regulate secondary metabolic pathways like antibiotic production. For instance, in the antibiotic producer Streptomyces fradiae, a layered network of TetRs regulate the levels of commercially important antibiotic tylosin, with TylP occupying the top of this cascading network. TetRs exist in two functional states; the DNA-bound and the ligand-bound form, which are allosterically regulated. Here, to develop deeper insights into the factors that govern allostery, the crystal structure of TylP was solved to a resolution of 2.3 A. The structure reveals that TylP possesses several unique features; notably, it harbors an unique C-terminal helix-loop extension that spans the entire length of the structure. This anchor connects the DNA binding domain (DBD) with the ligand binding domain (LBD) via a mix of positively charged and hydrogen-bonding interactions. Supporting EMSA studies with a series of DeltaC truncated versions show that a systematic deletion of this region results in complete loss of DNA binding. The structure additionally reveals that TylP is markedly different in the orientation of its DBD, LBD architecture and the dimeric geometry, from its hypothesized Streptomyces homologue CprB, which is a gamma- butyrolactone regulator. Rather, TylP is closer in structural design to macrolide binding TetRs, found in pathogens. Supporting MD studies suggest that TylP binds a macrolide intermediate in the tylosin pathway. Collectively, the structure along with corroborating biochemical studies provides insights into the novel mode of regulation of TetRs in antibiotic producing organisms.

-	~~Authors: Ray~~, S., ~~Panjikar~~, S., ~~Anand~~, R.	+	Functional Insights into the Mode of DNA and Ligand Binding of the TetR Family Regulator TylP from Streptomyces fradiae.,Ray S, Maitra A, Biswas A, Panjikar S, Mondal J, Anand R J Biol Chem. 2017 Jul 24. pii: jbc.M117.788000. doi: 10.1074/jbc.M117.788000. PMID:28739805<ref>PMID:28739805</ref>

-	~~Description: Crystal structure of full length native tylp~~, a ~~tetr regulator from streptomyces fradiae~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Panjikar, S]]~~	+	<div class="pdbe-citations 5xaz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Anand, R]]		[[Category: Anand, R]]
		+	[[Category: Panjikar, S]]
	[[Category: Ray, S]]		[[Category: Ray, S]]
		+	[[Category: Antibiotic regulation]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Hth dna binding domain]]
		+	[[Category: Tetr family]]
		+	[[Category: Transcription regulator]]

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

2017-04-05T12:26:05Z

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

←Older revision

Revision as of 12:26, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xaz is ON HOLD until Paper Publication Authors: Ray, S., Panjikar, S., Anand, R. Description: Crystal structure of full length native tylp, a tetr...

2017-04-05T12:26:03Z

New page: '''Unreleased structure''' The entry 5xaz is ON HOLD until Paper Publication Authors: Ray, S., Panjikar, S., Anand, R. Description: Crystal structure of full length native tylp, a tetr...

New page

'''Unreleased structure'''

The entry 5xaz is ON HOLD until Paper Publication

Authors: Ray, S., Panjikar, S., Anand, R.

Description: Crystal structure of full length native tylp, a tetr regulator from streptomyces fradiae
[[Category: Unreleased Structures]]
[[Category: Panjikar, S]]
[[Category: Anand, R]]
[[Category: Ray, S]]