6r5v - Revision history

OCA at 12:15, 24 January 2024

2024-01-24T12:15:51Z

←Older revision		Revision as of 12:15, 24 January 2024
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	<StructureSection load='6r5v' size='340' side='right'caption='[[6r5v]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6r5v' size='340' side='right'caption='[[6r5v]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r5v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r5v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R5V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=~~XYP~~:~~BETA~~-D-~~XYLOPYRANOSE~~'>~~XYP~~</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]] 1.8Å</td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~bglX, PA1726 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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=6r5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5v OCA], [https://pdbe.org/6r5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r5v RCSB], [https://www.ebi.ac.uk/pdbsum/6r5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5v 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=6r5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5v OCA], [https://pdbe.org/6r5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r5v RCSB], [https://www.ebi.ac.uk/pdbsum/6r5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9I311_PSEAE Q9I311_PSEAE]
	<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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Batuecas~~, M T~~]]	+	[[Category: Batuecas MT]]
-	[[Category: Hermoso~~, J A]]~~	+	[[Category: Hermoso JA]]
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:05, 30 March 2022

2022-03-30T11:05:59Z

←Older revision		Revision as of 11:05, 30 March 2022
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	==The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with xylotriose==		==The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with xylotriose==
-	<StructureSection load='6r5v' size='340' side='right'caption='[[6r5v]]' scene=''>	+	<StructureSection load='6r5v' size='340' side='right'caption='[[6r5v]], [[Resolution\|resolution]] 1.80Å' 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=6R5V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6R5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r5v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R5V 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=6r5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5v OCA], [~~http~~://pdbe.org/6r5v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r5v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r5v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5v 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bglX, PA1726 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=6r5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5v OCA], [https://pdbe.org/6r5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r5v RCSB], [https://www.ebi.ac.uk/pdbsum/6r5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5v ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BglX is a heretofore uncharacterized periplasmic glycoside hydrolase (GH) of the human pathogen Pseudomonas aeruginosa. X-ray analysis identifies it as a protein homodimer. The two active sites of the homodimer comprise catalytic residues provided by each monomer. This arrangement is seen in <2% of the hydrolases of known structure. In vitro substrate profiling shows BglX is a catalyst for beta-(1-->2) and beta-(1-->3) saccharide hydrolysis. Saccharides with beta-(1-->4) or beta-(1-->6) bonds, and the beta-(1-->4) muropeptides from the cell-wall peptidoglycan, are not substrates. Additional structural insights from X-ray analysis (including structures of a mutant enzyme-derived Michaelis complex, two transition-state mimetics, and two enzyme-product complexes) enabled the comprehensive description of BglX catalysis. The half-chair ((4)H3) conformation of the transition-state oxocarbenium species, the approach of the hydrolytic water molecule to the oxocarbenium species, and the stepwise release of the two reaction products were also visualized. The substrate pattern for BglX aligns with the [beta-(1-->2)-Glc]x and [beta-(1-->3)-Glc]x periplasmic osmoregulated periplasmic glucans, and possibly with the Psl exopolysaccharides, of P. aeruginosa. Both polysaccharides are implicated in biofilm formation. Accordingly, we show that inactivation of the bglX gene of P. aeruginosa PAO1 attenuates biofilm formation.
		+
		+	Catalytic Cycle of Glycoside Hydrolase BglX from Pseudomonas aeruginosa and Its Implications for Biofilm Formation.,Mahasenan KV, Batuecas MT, De Benedetti S, Kim C, Rana N, Lee M, Hesek D, Fisher JF, Sanz-Aparicio J, Hermoso JA, Mobashery S ACS Chem Biol. 2020 Jan 17;15(1):189-196. doi: 10.1021/acschembio.9b00754. Epub, 2020 Jan 7. PMID:31877028<ref>PMID:31877028</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6r5v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-glucosidase 3D structures\|Beta-glucosidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Batuecas MT]]	+	[[Category: Pseae]]
-	[[Category: Hermoso JA]]	+	[[Category: Batuecas, M T]]
		+	[[Category: Hermoso, J A]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA at 06:56, 15 April 2020

2020-04-15T06:56:17Z

←Older revision		Revision as of 06:56, 15 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6r5v is ON HOLD until Paper Publication~~	+	==The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with xylotriose==
-		+	<StructureSection load='6r5v' size='340' side='right'caption='[[6r5v]]' scene=''>
-	~~Authors: Batuecas, M.T., Hermoso, J.A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6R5V FirstGlance]. <br>
-	~~Description:~~ The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with xylotriose	+	</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=6r5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5v OCA], [http://pdbe.org/6r5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r5v RCSB], [http://www.ebi.ac.uk/pdbsum/6r5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5v ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Hermoso~~, J.A]]	+	__TOC__
-	[[Category: Batuecas~~, M.T~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Batuecas MT]]
		+	[[Category: Hermoso JA]]

OCA: Protected "6r5v" [edit=sysop:move=sysop]

2019-04-03T05:00:28Z

Protected "6r5v" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:00, 3 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r5v is ON HOLD until Paper Publication Authors: Batuecas, M.T., Hermoso, J.A. Description: The crystal structure of Glycoside Hydrolase BglX inact...

2019-04-03T05:00:25Z

New page: '''Unreleased structure''' The entry 6r5v is ON HOLD until Paper Publication Authors: Batuecas, M.T., Hermoso, J.A. Description: The crystal structure of Glycoside Hydrolase BglX inact...

New page

'''Unreleased structure'''

The entry 6r5v is ON HOLD until Paper Publication

Authors: Batuecas, M.T., Hermoso, J.A.

Description: The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with xylotriose
[[Category: Unreleased Structures]]
[[Category: Hermoso, J.A]]
[[Category: Batuecas, M.T]]