5ohs - Revision history

OCA at 07:27, 1 May 2024

OCA — Wed, 01 May 2024 07:27:50 GMT

←Older revision		Revision as of 07:27, 1 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A083ZKV2_RHIRD A0A083ZKV2_RHIRD]		[https://www.uniprot.org/uniprot/A0A083ZKV2_RHIRD A0A083ZKV2_RHIRD]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	An estimated 10 billion tonnes of sulfoquinovose (SQ) are produced and degraded each year. Prokaryotic sulfoglycolytic pathways catabolize sulfoquinovose (SQ) liberated from plant sulfolipid, or its delipidated form alpha-d-sulfoquinovosyl glycerol (SQGro), through the action of a sulfoquinovosidase (SQase), but little is known about the capacity of SQ glycosides to support growth. Structural studies of the first reported SQase (Escherichia coli YihQ) have identified three conserved residues that are essential for substrate recognition, but crossover mutations exploring active-site residues of predicted SQases from other organisms have yielded inactive mutants casting doubt on bioinformatic functional assignment. Here, we show that SQGro can support the growth of E. coli on par with d-glucose, and that the E. coli SQase prefers the naturally occurring diastereomer of SQGro. A predicted, but divergent, SQase from Agrobacterium tumefaciens proved to have highly specific activity toward SQ glycosides, and structural, mutagenic, and bioinformatic analyses revealed the molecular coevolution of catalytically important amino acid pairs directly involved in substrate recognition, as well as structurally important pairs distal to the active site. Understanding the defining features of SQases empowers bioinformatic approaches for mapping sulfur metabolism in diverse microbial communities and sheds light on this poorly understood arm of the biosulfur cycle.
-
-	Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases.,Abayakoon P, Jin Y, Lingford JP, Petricevic M, John A, Ryan E, Wai-Ying Mui J, Pires DEV, Ascher DB, Davies GJ, Goddard-Borger ED, Williams SJ ACS Cent Sci. 2018 Sep 26;4(9):1266-1273. doi: 10.1021/acscentsci.8b00453. Epub, 2018 Sep 5. PMID:30276262<ref>PMID:30276262</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5ohs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]		*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:50, 13 December 2023

OCA — Wed, 13 Dec 2023 16:50:41 GMT

←Older revision		Revision as of 16:50, 13 December 2023
Line 1:		Line 1:

	==A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ==		==A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ==
-	<StructureSection load='5ohs' size='340' side='right' caption='[[5ohs]], [[Resolution\|resolution]] 1.97Å' scene=''>	+	<StructureSection load='5ohs' size='340' side='right'caption='[[5ohs]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ohs]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OHS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ohs]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OHS 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NSQ:4-NITROPHENYL-ALPHA-D-SULFOQUINOVOSIDE'>NSQ</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 1.97Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SY94_3281 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NSQ:4-NITROPHENYL-ALPHA-D-SULFOQUINOVOSIDE'>NSQ</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=5ohs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohs OCA], [https://pdbe.org/5ohs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ohs RCSB], [https://www.ebi.ac.uk/pdbsum/5ohs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohs ProSAT]</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=5ohs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohs OCA], [~~http~~://pdbe.org/5ohs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ohs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ohs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohs ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A083ZKV2_RHIRD A0A083ZKV2_RHIRD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ohs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ohs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alpha-glucosidase~~]]	+	[[Category: Agrobacterium tumefaciens]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Large Structures]]
-	[[Category: Goddard-Borger, E]]	+	[[Category: Davies GJ]]
-	[[Category: Jin, Y]]	+	[[Category: Goddard-Borger E]]
-	[[Category: Williams~~, S J]]~~	+	[[Category: Jin Y]]
-	~~[[Category: Complex]]~~	+	[[Category: Williams SJ]]
-	~~[[Category: General acid-base varient]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Sulfoglycolysis]]~~	+
-	~~[[Category: Sulfoglycosidase~~]]	+

OCA at 07:31, 21 February 2019

OCA — Thu, 21 Feb 2019 07:31:16 GMT

←Older revision		Revision as of 07:31, 21 February 2019
Line 1:		Line 1:

-	==GH31 ~~glycosidase variant -~~ D455N==	+	==A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ==
	<StructureSection load='5ohs' size='340' side='right' caption='[[5ohs]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='5ohs' size='340' side='right' caption='[[5ohs]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ohs]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OHS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ohs]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OHS 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NSQ:4-NITROPHENYL-ALPHA-D-SULFOQUINOVOSIDE'>NSQ</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NSQ:4-NITROPHENYL-ALPHA-D-SULFOQUINOVOSIDE'>NSQ</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SY94_3281 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=5ohs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohs OCA], [http://pdbe.org/5ohs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohs RCSB], [http://www.ebi.ac.uk/pdbsum/5ohs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohs ProSAT]</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=5ohs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohs OCA], [http://pdbe.org/5ohs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohs RCSB], [http://www.ebi.ac.uk/pdbsum/5ohs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohs ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	An estimated 10 billion tonnes of sulfoquinovose (SQ) are produced and degraded each year. Prokaryotic sulfoglycolytic pathways catabolize sulfoquinovose (SQ) liberated from plant sulfolipid, or its delipidated form alpha-d-sulfoquinovosyl glycerol (SQGro), through the action of a sulfoquinovosidase (SQase), but little is known about the capacity of SQ glycosides to support growth. Structural studies of the first reported SQase (Escherichia coli YihQ) have identified three conserved residues that are essential for substrate recognition, but crossover mutations exploring active-site residues of predicted SQases from other organisms have yielded inactive mutants casting doubt on bioinformatic functional assignment. Here, we show that SQGro can support the growth of E. coli on par with d-glucose, and that the E. coli SQase prefers the naturally occurring diastereomer of SQGro. A predicted, but divergent, SQase from Agrobacterium tumefaciens proved to have highly specific activity toward SQ glycosides, and structural, mutagenic, and bioinformatic analyses revealed the molecular coevolution of catalytically important amino acid pairs directly involved in substrate recognition, as well as structurally important pairs distal to the active site. Understanding the defining features of SQases empowers bioinformatic approaches for mapping sulfur metabolism in diverse microbial communities and sheds light on this poorly understood arm of the biosulfur cycle.
		+
		+	Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases.,Abayakoon P, Jin Y, Lingford JP, Petricevic M, John A, Ryan E, Wai-Ying Mui J, Pires DEV, Ascher DB, Davies GJ, Goddard-Borger ED, Williams SJ ACS Cent Sci. 2018 Sep 26;4(9):1266-1273. doi: 10.1021/acscentsci.8b00453. Epub, 2018 Sep 5. PMID:30276262<ref>PMID:30276262</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ohs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:14, 9 August 2018

OCA — Thu, 09 Aug 2018 21:14:15 GMT

←Older revision		Revision as of 21:14, 9 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ohs is ~~ON HOLD until Paper Publication~~	+	==GH31 glycosidase variant - D455N==
-		+	<StructureSection load='5ohs' size='340' side='right' caption='[[5ohs]], [[Resolution\|resolution]] 1.97Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ohs]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OHS FirstGlance]. <br>
-	~~Description~~:	+	</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NSQ:4-NITROPHENYL-ALPHA-D-SULFOQUINOVOSIDE'>NSQ</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-glucosidase Alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.20 3.2.1.20] </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=5ohs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohs OCA], [http://pdbe.org/5ohs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohs RCSB], [http://www.ebi.ac.uk/pdbsum/5ohs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohs ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alpha-glucosidase]]
		+	[[Category: Davies, G J]]
		+	[[Category: Goddard-Borger, E]]
		+	[[Category: Jin, Y]]
		+	[[Category: Williams, S J]]
		+	[[Category: Complex]]
		+	[[Category: General acid-base varient]]
		+	[[Category: Hydrolase]]
		+	[[Category: Sulfoglycolysis]]
		+	[[Category: Sulfoglycosidase]]

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

OCA — Wed, 27 Sep 2017 12:26:52 GMT

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

←Older revision

Revision as of 12:26, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ohs is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 12:26:51 GMT

New page: '''Unreleased structure''' The entry 5ohs is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ohs is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]