6tyr - Revision history

OCA at 07:40, 11 October 2023

OCA — Wed, 11 Oct 2023 07:40:29 GMT

←Older revision		Revision as of 07:40, 11 October 2023
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	<StructureSection load='6tyr' size='340' side='right'caption='[[6tyr]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='6tyr' size='340' side='right'caption='[[6tyr]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tyr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet2 Thet2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tyr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TYR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>~~, ~~<scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.813Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~TT_C1370 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=262724 THET2])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Laccase Laccase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.2 1.10.3.2]~~ </~~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=6tyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyr OCA], [https://pdbe.org/6tyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tyr RCSB], [https://www.ebi.ac.uk/pdbsum/6tyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyr 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=6tyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyr OCA], [https://pdbe.org/6tyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tyr RCSB], [https://www.ebi.ac.uk/pdbsum/6tyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyr ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72HW2_THET2 Q72HW2_THET2]
	<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: Laccase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet2~~]]	+	[[Category: Thermus thermophilus HB27]]
-	[[Category: Miranda-Blancas, R]]	+	[[Category: Miranda-Blancas R]]
-	[[Category: Rudino-Pinera, E]]	+	[[Category: Rudino-Pinera E]]
-	~~[[Category: Close loop]]~~	+
-	~~[[Category: Multicopper oxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:25, 25 August 2021

OCA — Wed, 25 Aug 2021 06:25:42 GMT

←Older revision		Revision as of 06:25, 25 August 2021
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	==Crystal structure of Laccase from Thermus thermophilus HB27 with a close conformation of its beta-hairpin==		==Crystal structure of Laccase from Thermus thermophilus HB27 with a close conformation of its beta-hairpin==
-	<StructureSection load='6tyr' size='340' side='right'caption='[[6tyr]]' scene=''>	+	<StructureSection load='6tyr' size='340' side='right'caption='[[6tyr]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tyr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TYR FirstGlance]. <br>
-	</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=6tyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyr OCA], [~~http~~://pdbe.org/6tyr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tyr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tyr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyr ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C1370 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Laccase Laccase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.2 1.10.3.2] </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=6tyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyr OCA], [https://pdbe.org/6tyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tyr RCSB], [https://www.ebi.ac.uk/pdbsum/6tyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyr ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The multi-copper oxidase from the hyper-thermophilic bacteria Thermus thermophilus (Tth-MCO), has been previously characterized and described as an example of a laccase with low catalytic properties, especially when it is compared with the activity of fungal laccases, but it is active at high temperatures. Structurally, Tth-MCO has a unique feature: a beta-hairpin near the T1Cu site, which is not present in any other laccases deposited at the PDB. This beta-hairpin has an expected crystallographic behavior in solvent-exposed areas of a crystallized protein: lack of electron density, high B-values and several crystalline contacts with neighboring crystallographic copies; however, its dynamical behavior in solution and its biological implications have not been described. Here, we describe four new Tth-MCO crystallographic structures, and the beta-hairpin behavior has been analyzed by molecular dynamics simulations, considering the effect of pH and temperature. The beta-hairpin new crystallographic conformations described here, together with their dynamics, were used to understand the pH-restrained laccase activity of Tth-MCO against substrates as syringaldazine. Remarkably, there are insertions in laccases from Thermus and Meiothermus genus, sharing the same position and a methionine-rich composition of the Tth-MCO beta-hairpin. This unique high methionine content of the Tth-MCO beta-hairpin is responsible to coordinate, Ag(+1) and Hg(+1) in oxidative conditions, but Cu(+1) and Cu(+2) are not coordinated in crystallographic experiments, regardless of the redox conditions; however, Ag(+1) addition does not affect Tth-MCO laccase activity against syringaldazine. Here, we propose that the pH-dependent beta-hairpin dynamical behavior could explain, at least in part, the inefficient laccase activity displayed by Tth-MCO in acidic pH values.
		+
		+	The beta-hairpin from the Thermus thermophilus HB27 laccase works as a pH-dependent switch to regulate laccase activity.,Miranda-Blancas R, Avelar M, Rodriguez-Arteaga A, Sinicropi A, Rudino-Pinera E J Struct Biol. 2021 Jun;213(2):107740. doi: 10.1016/j.jsb.2021.107740. Epub 2021 , May 5. PMID:33962016<ref>PMID:33962016</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tyr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Laccase 3D structures\|Laccase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Laccase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Miranda-Blancas R]]	+	[[Category: Thet2]]
-	[[Category: Rudino-Pinera E]]	+	[[Category: Miranda-Blancas, R]]
		+	[[Category: Rudino-Pinera, E]]
		+	[[Category: Close loop]]
		+	[[Category: Multicopper oxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 09:46, 12 August 2020

OCA — Wed, 12 Aug 2020 09:46:49 GMT

←Older revision		Revision as of 09:46, 12 August 2020
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-	'''Unreleased structure'''

-	~~The entry 6tyr is ON HOLD until Aug 09 2021~~	+	==Crystal structure of Laccase from Thermus thermophilus HB27 with a close conformation of its beta-hairpin==
-		+	<StructureSection load='6tyr' size='340' side='right'caption='[[6tyr]]' scene=''>
-	~~Authors: Miranda-Blancas, R., Rudino-Pinera, E.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TYR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TYR FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Laccase from Thermus thermophilus HB27 with a close conformation of its beta-hairpin	+	</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=6tyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tyr OCA], [http://pdbe.org/6tyr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tyr RCSB], [http://www.ebi.ac.uk/pdbsum/6tyr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tyr ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Miranda-Blancas, R]]	+	__TOC__
-	[[Category: Rudino-Pinera, E]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Miranda-Blancas R]]
		+	[[Category: Rudino-Pinera E]]

OCA at 07:23, 1 April 2020

OCA — Wed, 01 Apr 2020 07:23:18 GMT

←Older revision		Revision as of 07:23, 1 April 2020
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	Authors: Miranda-Blancas, R., Rudino-Pinera, E.		Authors: Miranda-Blancas, R., Rudino-Pinera, E.

-	Description: ~~Dynamic behavior of alpha-beta loop at laccase~~ of Thermus thermophilus.	+	Description: Crystal structure of Laccase from Thermus thermophilus HB27 with a close conformation of its beta-hairpin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Miranda-Blancas, R]]		[[Category: Miranda-Blancas, R]]
	[[Category: Rudino-Pinera, E]]		[[Category: Rudino-Pinera, E]]

OCA at 03:51, 10 October 2019

OCA — Thu, 10 Oct 2019 03:51:00 GMT

←Older revision		Revision as of 03:51, 10 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6tyr is ON HOLD	+	The entry 6tyr is ON HOLD until Aug 09 2021

	Authors: Miranda-Blancas, R., Rudino-Pinera, E.		Authors: Miranda-Blancas, R., Rudino-Pinera, E.

OCA: Protected "6tyr" [edit=sysop:move=sysop]

OCA — Wed, 21 Aug 2019 04:23:26 GMT

Protected "6tyr" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:23, 21 August 2019

OCA: New page: '''Unreleased structure''' The entry 6tyr is ON HOLD Authors: Miranda-Blancas, R., Rudino-Pinera, E. Description: Dynamic behavior of alpha-beta loop at laccase of Thermus thermophilus...

OCA — Wed, 21 Aug 2019 04:23:25 GMT

New page: '''Unreleased structure''' The entry 6tyr is ON HOLD Authors: Miranda-Blancas, R., Rudino-Pinera, E. Description: Dynamic behavior of alpha-beta loop at laccase of Thermus thermophilus...

New page

'''Unreleased structure'''

The entry 6tyr is ON HOLD

Authors: Miranda-Blancas, R., Rudino-Pinera, E.

Description: Dynamic behavior of alpha-beta loop at laccase of Thermus thermophilus.
[[Category: Unreleased Structures]]
[[Category: Miranda-Blancas, R]]
[[Category: Rudino-Pinera, E]]