3zjk - Revision history

OCA at 11:03, 20 December 2023

OCA — Wed, 20 Dec 2023 11:03:17 GMT

←Older revision		Revision as of 11:03, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='3zjk' size='340' side='right'caption='[[3zjk]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3zjk' size='340' side='right'caption='[[3zjk]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zjk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zjk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZJK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.2Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=3zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zjk OCA], [https://pdbe.org/3zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zjk RCSB], [https://www.ebi.ac.uk/pdbsum/3zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zjk 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=3zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zjk OCA], [https://pdbe.org/3zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zjk RCSB], [https://www.ebi.ac.uk/pdbsum/3zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zjk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RA61_THETH Q9RA61_THETH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: Beta-glucosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Czjzek, M]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Dion, M]]	+	[[Category: Czjzek M]]
-	[[Category: Leroux, C]]	+	[[Category: Dion M]]
-	[[Category: Roncza, J]]	+	[[Category: Leroux C]]
-	[[Category: Tellier, C]]	+	[[Category: Roncza J]]
-	[[Category: Teze, D]]	+	[[Category: Tellier C]]
-	[[Category: Tran, V]]	+	[[Category: Teze D]]
-	~~[[Category: Glycoside hydrolase family 1]]~~	+	[[Category: Tran V]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Transglycosidase~~]]	+

OCA at 05:48, 10 August 2022

OCA — Wed, 10 Aug 2022 05:48:37 GMT

←Older revision		Revision as of 05:48, 10 August 2022
Line 1:		Line 1:

	==crystal structure of Ttb-gly F401S mutant==		==crystal structure of Ttb-gly F401S mutant==
-	<StructureSection load='3zjk' size='340' side='right' caption='[[3zjk]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='3zjk' size='340' side='right'caption='[[3zjk]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zjk]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zjk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZJK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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'>[~~http~~://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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=3zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zjk OCA], [~~http~~://pdbe.org/3zjk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zjk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zjk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zjk 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=3zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zjk OCA], [https://pdbe.org/3zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zjk RCSB], [https://www.ebi.ac.uk/pdbsum/3zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zjk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Beta-glucosidase]]		[[Category: Beta-glucosidase]]
		+	[[Category: Large Structures]]
	[[Category: Czjzek, M]]		[[Category: Czjzek, M]]
	[[Category: Dion, M]]		[[Category: Dion, M]]

OCA at 16:10, 11 August 2016

OCA — Thu, 11 Aug 2016 16:10:26 GMT

←Older revision		Revision as of 16:10, 11 August 2016
Line 1:		Line 1:
		+
	==crystal structure of Ttb-gly F401S mutant==		==crystal structure of Ttb-gly F401S mutant==
	<StructureSection load='3zjk' size='340' side='right' caption='[[3zjk]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3zjk' size='340' side='right' caption='[[3zjk]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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=3zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zjk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zjk RCSB], [http://www.ebi.ac.uk/pdbsum/3zjk 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=3zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zjk OCA], [http://pdbe.org/3zjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zjk RCSB], [http://www.ebi.ac.uk/pdbsum/3zjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zjk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3zjk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:31, 4 January 2015

OCA — Sun, 04 Jan 2015 09:31:03 GMT

←Older revision		Revision as of 09:31, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3zjk\| PDB=3zjk \| SCENE= }}~~	+	==crystal structure of Ttb-gly F401S mutant==
-	===crystal structure of Ttb-gly F401S mutant===	+	<StructureSection load='3zjk' size='340' side='right' caption='[[3zjk]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24287187}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3zjk]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZJK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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'>[http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] </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=3zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zjk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zjk RCSB], [http://www.ebi.ac.uk/pdbsum/3zjk PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A large number of retaining glycosidases catalyze both hydrolysis and transglycosylation reactions, but little is known about what determines the balance between these two activities (transglycosylation/hydrolysis ratio). We previously obtained by directed evolution the mutants F401S and N282T of Thermus thermophilus beta-glycosidase (Ttbeta-gly, glycoside hydrolase family 1 (GH1)), which display a higher transglycosylation/hydrolysis ratio than the wild-type enzyme. In order to find the cause of these activity modifications, and thereby set up a generic method for easily obtaining transglycosidases from glycosidases, we determined their X-ray structure. No major structural changes could be observed which could help to rationalize the mutagenesis of glycosidases into transglycosidases. However, as these mutations are highly conserved in GH1 beta-glycosidases and are located around the -1 site, we pursued the isolation of new transglycosidases by targeting highly conserved amino acids located around the active site. Thus, by single-point mutagenesis on Ttbeta-gly, we created four new mutants that exhibit improved synthetic activity, producing disaccharides in yields of 68-90% against only 36% when native Ttbeta-gly was used. As all of the chosen positions were well conserved among GH1 enzymes, this approach is most probably a general route to convert GH1 glycosidases into transglycosidases.

-	~~==About this Structure==~~	+	Semi-rational approach for converting a GH1 beta-glycosidase into a beta-transglycosidase.,Teze D, Hendrickx J, Czjzek M, Ropartz D, Sanejouand YH, Tran V, Tellier C, Dion M Protein Eng Des Sel. 2014 Jan;27(1):13-9. doi: 10.1093/protein/gzt057. Epub 2013 , Nov 27. PMID:24287187<ref>PMID:24287187</ref>
-	~~[[3zjk]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3ZJK OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024287187</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Beta-glucosidase]]		[[Category: Beta-glucosidase]]
-	[[Category: Czjzek, M.]]	+	[[Category: Czjzek, M]]
-	[[Category: Dion, M.]]	+	[[Category: Dion, M]]
-	[[Category: Leroux, C.]]	+	[[Category: Leroux, C]]
-	[[Category: Roncza, J.]]	+	[[Category: Roncza, J]]
-	[[Category: Tellier, C.]]	+	[[Category: Tellier, C]]
-	[[Category: Teze, D.]]	+	[[Category: Teze, D]]
-	[[Category: Tran, V.]]	+	[[Category: Tran, V]]
	[[Category: Glycoside hydrolase family 1]]		[[Category: Glycoside hydrolase family 1]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Transglycosidase]]		[[Category: Transglycosidase]]

OCA at 09:07, 5 February 2014

OCA — Wed, 05 Feb 2014 09:07:42 GMT

←Older revision		Revision as of 09:07, 5 February 2014
Line 1:		Line 1:
-	[[Image:3zjk.jpg\|left\|200px]]
-
	{{STRUCTURE_3zjk\| PDB=3zjk \| SCENE= }}		{{STRUCTURE_3zjk\| PDB=3zjk \| SCENE= }}
-
	===crystal structure of Ttb-gly F401S mutant===		===crystal structure of Ttb-gly F401S mutant===
		+	{{ABSTRACT_PUBMED_24287187}}

		+	==About this Structure==
		+	[[3zjk]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA].

-	==~~About this Structure~~==	+	==Reference==
-	~~[[3zjk]] is a 3 chain structure with sequence from [http~~://~~en.wikipedia.org~~/~~wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from~~ [~~http~~:~~//oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA~~].	+	<ref group="xtra">PMID:024287187</ref><references group="xtra"/><references/>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Beta-glucosidase]]		[[Category: Beta-glucosidase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Czjzek, M.]]		[[Category: Czjzek, M.]]
	[[Category: Dion, M.]]		[[Category: Dion, M.]]

OCA at 10:38, 13 February 2013

OCA — Wed, 13 Feb 2013 10:38:11 GMT

←Older revision		Revision as of 10:38, 13 February 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3zjk.jpg\|left\|200px]]

-	~~The entry~~ 3zjk ~~is ON HOLD~~	+	{{STRUCTURE_3zjk\| PDB=3zjk \| SCENE= }}

-	~~Authors: Teze, D., Tran, V., Tellier, C., Dion, M., Leroux, C., Roncza, J., Czjzek, M.~~	+	===crystal structure of Ttb-gly F401S mutant===

-	~~Description: crystal~~ structure ~~of Ttb~~-~~gly F401S mutant~~	+
		+	==About this Structure==
		+	[[3zjk]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZJK OCA].
		+	[[Category: Beta-glucosidase]]
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Czjzek, M.]]
		+	[[Category: Dion, M.]]
		+	[[Category: Leroux, C.]]
		+	[[Category: Roncza, J.]]
		+	[[Category: Tellier, C.]]
		+	[[Category: Teze, D.]]
		+	[[Category: Tran, V.]]
		+	[[Category: Glycoside hydrolase family 1]]
		+	[[Category: Hydrolase]]
		+	[[Category: Transglycosidase]]

OCA: Protected "3zjk" [edit=sysop:move=sysop]

OCA — Wed, 23 Jan 2013 10:58:10 GMT

Protected "3zjk" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:58, 23 January 2013

OCA: New page: '''Unreleased structure''' The entry 3zjk is ON HOLD Authors: Teze, D., Tran, V., Tellier, C., Dion, M., Leroux, C., Roncza, J., Czjzek, M. Description: crystal structure of Ttb-gly F4...

OCA — Wed, 23 Jan 2013 10:58:09 GMT

New page: '''Unreleased structure''' The entry 3zjk is ON HOLD Authors: Teze, D., Tran, V., Tellier, C., Dion, M., Leroux, C., Roncza, J., Czjzek, M. Description: crystal structure of Ttb-gly F4...

New page

'''Unreleased structure'''

The entry 3zjk is ON HOLD

Authors: Teze, D., Tran, V., Tellier, C., Dion, M., Leroux, C., Roncza, J., Czjzek, M.

Description: crystal structure of Ttb-gly F401S mutant