5nav - Revision history

OCA at 12:43, 15 November 2023

OCA — Wed, 15 Nov 2023 12:43:36 GMT

←Older revision		Revision as of 12:43, 15 November 2023
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	<StructureSection load='5nav' size='340' side='right'caption='[[5nav]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5nav' size='340' side='right'caption='[[5nav]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nav]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NAV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5NAV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nav]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum Lactiplantibacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NAV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NAV FirstGlance]. <br>
-	</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>	+	</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=5nav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nav OCA], [~~http~~://pdbe.org/5nav PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nav RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nav PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nav 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=5nav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nav OCA], [https://pdbe.org/5nav PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nav RCSB], [https://www.ebi.ac.uk/pdbsum/5nav PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nav ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F9ULH8_LACPL F9ULH8_LACPL]
	<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: ~~Beta-glucosidase~~]]	+	[[Category: Lactiplantibacillus plantarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Acebron, I]]	+	[[Category: Acebron I]]
-	[[Category: Mancheno~~, J M]]~~	+	[[Category: Mancheno JM]]
-	~~[[Category: Cysteine residue]]~~	+
-	~~[[Category: Glycoside]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein aggregation]]~~	+
-	~~[[Category: Reducing agent]]~~	+
-	~~[[Category: Solubility enhancer~~]]	+

OCA at 12:01, 26 August 2020

OCA — Wed, 26 Aug 2020 12:01:04 GMT

←Older revision		Revision as of 12:01, 26 August 2020
Line 1:		Line 1:

	==Crystal structure of the double mutant (Cys211Ser/Cys292Ser) 6-phospho-b-D-glucosidase from Lactobacillus plantarum==		==Crystal structure of the double mutant (Cys211Ser/Cys292Ser) 6-phospho-b-D-glucosidase from Lactobacillus plantarum==
-	<StructureSection load='5nav' size='340' side='right' caption='[[5nav]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5nav' size='340' side='right'caption='[[5nav]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nav]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NAV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NAV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nav]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NAV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NAV FirstGlance]. <br>
	</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>		</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=5nav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nav OCA], [http://pdbe.org/5nav PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nav RCSB], [http://www.ebi.ac.uk/pdbsum/5nav PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nav 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=5nav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nav OCA], [http://pdbe.org/5nav PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nav RCSB], [http://www.ebi.ac.uk/pdbsum/5nav PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nav ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5nav" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5nav" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Beta-glucosidase]]		[[Category: Beta-glucosidase]]
		+	[[Category: Large Structures]]
	[[Category: Acebron, I]]		[[Category: Acebron, I]]
	[[Category: Mancheno, J M]]		[[Category: Mancheno, J M]]

OCA at 03:53, 4 August 2017

OCA — Fri, 04 Aug 2017 03:53:30 GMT

←Older revision		Revision as of 03:53, 4 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nav is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the double mutant (Cys211Ser/Cys292Ser) 6-phospho-b-D-glucosidase from Lactobacillus plantarum==
		+	<StructureSection load='5nav' size='340' side='right' caption='[[5nav]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5nav]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NAV FirstGlance]. <br>
		+	</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=5nav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nav OCA], [http://pdbe.org/5nav PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nav RCSB], [http://www.ebi.ac.uk/pdbsum/5nav PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nav ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Statistics from structural genomics initiatives reveal that around 50-55% of the expressed, non-membrane proteins cannot be purified and therefore structurally characterized due to solubility problems, which emphasized protein solubility as one of the most serious concerns in structural biology projects. Lactobacillus plantarum CECT 748T produces an aggregation-prone glycosidase (LpBgl) that we crystallized previously. However, this result could not be reproduced due to protein instability and therefore further high-resolution structural analyses of LpBgl were impeded. The obtained crystals of LpBgl diffracted up to 2.48A resolution and permitted to solve the structure of the enzyme. Analysis of the active site revealed a pocket for phosphate-binding with an uncommon architecture, where a phosphate molecule is tightly bound suggesting the recognition of 6-phosphoryl sugars. In agreement with this observation, we showed that LpBgl exhibited 6-phospho-beta-glucosidase activity. Combination of structural and mass spectrometry results revealed the formation of dimethyl arsenic adducts on the solvent exposed cysteine residues Cys211 and Cys292. Remarkably, the double mutant Cys211Ser/Cys292Ser resulted stable in solution at high concentrations indicating that the marginal solubility of LpBgl can be ascribed specifically to these two cysteine residues. The 2.30A crystal structure of this double mutant showed no disorder around the newly incorporated serine residues and also loop rearrangements within the phosphate-binding site. Notably, LpBgl could be prepared at high yield by proteolytic digestion of the fusion protein LSLt-LpBgl, which raises important questions about potential hysteretic processes upon its initial production as an enzyme fused to a solubility enhancer.

-	~~Authors: Acebron~~, I., ~~Mancheno~~, J.M.	+	Structural basis of the substrate specificity and instability in solution of a glycosidase from Lactobacillus plantarum.,Acebron I, Plaza-Vinuesa L, de Las Rivas B, Munoz R, Cumella J, Sanchez-Sancho F, Mancheno JM Biochim Biophys Acta. 2017 Jul 19;1865(10):1227-1236. doi:, 10.1016/j.bbapap.2017.07.007. PMID:28734976<ref>PMID:28734976</ref>

-	~~Description: Crystal structure~~ of the ~~double mutant (Cys211Ser~~/~~Cys292Ser) 6~~-~~phospho~~-~~b-D-glucosidase from Lactobacillus plantarum~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Mancheno, J.M~~]]	+	<div class="pdbe-citations 5nav" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-glucosidase]]
	[[Category: Acebron, I]]		[[Category: Acebron, I]]
		+	[[Category: Mancheno, J M]]
		+	[[Category: Cysteine residue]]
		+	[[Category: Glycoside]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein aggregation]]
		+	[[Category: Reducing agent]]
		+	[[Category: Solubility enhancer]]

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

OCA — Thu, 09 Mar 2017 12:22:36 GMT

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

←Older revision

Revision as of 12:22, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5nav is ON HOLD until Paper Publication Authors: Acebron, I., Mancheno, J.M. Description: Crystal structure of the double mutant (Cys211Ser/Cys292S...

OCA — Thu, 09 Mar 2017 12:22:35 GMT

New page: '''Unreleased structure''' The entry 5nav is ON HOLD until Paper Publication Authors: Acebron, I., Mancheno, J.M. Description: Crystal structure of the double mutant (Cys211Ser/Cys292S...

New page

'''Unreleased structure'''

The entry 5nav is ON HOLD until Paper Publication

Authors: Acebron, I., Mancheno, J.M.

Description: Crystal structure of the double mutant (Cys211Ser/Cys292Ser) 6-phospho-b-D-glucosidase from Lactobacillus plantarum
[[Category: Unreleased Structures]]
[[Category: Mancheno, J.M]]
[[Category: Acebron, I]]