4rs3 - Revision history

OCA at 08:26, 8 March 2023

OCA — Wed, 08 Mar 2023 08:26:36 GMT

←Older revision		Revision as of 08:26, 8 March 2023
Line 1:		Line 1:

	==Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol==		==Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol==
-	<StructureSection load='4rs3' size='340' side='right' caption='[[4rs3]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='4rs3' size='340' side='right'caption='[[4rs3]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rs3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycs2 Mycs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RS3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rs3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RS3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=~~XYL~~:~~D-XYLITOL~~'>~~XYL~~</scene>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=4rs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs3 OCA], [https://pdbe.org/4rs3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rs3 RCSB], [https://www.ebi.ac.uk/pdbsum/4rs3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs3 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_3598, MSMEI_3515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Monosaccharide-transporting_ATPase Monosaccharide-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.17 3.6.3.17] </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=4rs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs3 OCA], [~~http~~://pdbe.org/4rs3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rs3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rs3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYPA_MYCS2 XYPA_MYCS2] Part of an ABC transporter complex likely involved in xylitol import. Binds xylitol.<ref>PMID:26560079</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Monosaccharide-transporting ATPase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mycs2~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Al Obaidi N]]
-	[[Category: Attonito~~, J D~~]]	+	[[Category: Almo SC]]
-	[[Category: Bhosle, R]]	+	[[Category: Attonito JD]]
-	[[Category: Chamala, S]]	+	[[Category: Bhosle R]]
-	[[Category: Chowdhury, S]]	+	[[Category: Chamala S]]
-	~~[[Category: EFI, Enzyme Function Initiative~~]]	+	[[Category: Chowdhury S]]
-	[[Category: Gerlt~~, J A]]~~	+	[[Category: Gerlt JA]]
-	~~[[Category: Glenn, A Scott~~]]	+	[[Category: Hillerich B]]
-	[[Category: Hillerich, B]]	+	[[Category: Lafleur J]]
-	[[Category: Lafleur, J]]	+	[[Category: Love J]]
-	[[Category: Love, J]]	+	[[Category: Morisco LL]]
-	[[Category: Morisco~~, L L~~]]	+	[[Category: Patskovsky Y]]
-	[[Category: ~~Obaidi, N Al~~]]	+	[[Category: Scott Glenn A]]
-	[[Category: ~~Patskovsky, Y~~]]	+	[[Category: Siedel RD]]
-	[[Category: Siedel~~, R D~~]]	+	[[Category: Toro R]]
-	[[Category: Toro, R]]	+	[[Category: Wasserman SR]]
-	[[Category: Wasserman~~, S R~~]]	+	[[Category: Whalen KL]]
-	[[Category: Whalen~~, K L]]~~	+
-	~~[[Category: Abc-type]]~~	+
-	~~[[Category: Efi]]~~	+
-	~~[[Category: Enzyme function initiative]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Sugar transporter]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 20:20, 24 January 2018

OCA — Wed, 24 Jan 2018 20:20:41 GMT

←Older revision		Revision as of 20:20, 24 January 2018
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	<StructureSection load='4rs3' size='340' side='right' caption='[[4rs3]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4rs3' size='340' side='right' caption='[[4rs3]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rs3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rs3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_3598, MSMEI_3515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Monosaccharide-transporting_ATPase Monosaccharide-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.17 3.6.3.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Monosaccharide-transporting_ATPase Monosaccharide-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.17 3.6.3.17] </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=4rs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs3 OCA], [http://pdbe.org/4rs3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rs3 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs3 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=4rs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs3 OCA], [http://pdbe.org/4rs3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rs3 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Monosaccharide-transporting ATPase]]		[[Category: Monosaccharide-transporting ATPase]]
		+	[[Category: Mycs2]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Attonito, J D]]		[[Category: Attonito, J D]]
Line 28:		Line 30:
	[[Category: Chamala, S]]		[[Category: Chamala, S]]
	[[Category: Chowdhury, S]]		[[Category: Chowdhury, S]]
-	[[Category: ~~Efi~~, Enzyme Function Initiative]]	+	[[Category: EFI, Enzyme Function Initiative]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]
	[[Category: Glenn, A Scott]]		[[Category: Glenn, A Scott]]

OCA at 07:44, 1 June 2016

OCA — Wed, 01 Jun 2016 07:44:10 GMT

←Older revision		Revision as of 07:44, 1 June 2016
Line 1:		Line 1:
		+
	==Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol==		==Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol==
	<StructureSection load='4rs3' size='340' side='right' caption='[[4rs3]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4rs3' size='340' side='right' caption='[[4rs3]], [[Resolution\|resolution]] 1.40Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Monosaccharide-transporting_ATPase Monosaccharide-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.17 3.6.3.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Monosaccharide-transporting_ATPase Monosaccharide-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.17 3.6.3.17] </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=4rs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rs3 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs3 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=4rs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs3 OCA], [http://pdbe.org/4rs3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rs3 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs3 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We describe a general integrated bioinformatic and experimental strategy to discover the in vitro enzymatic activities and in vivo functions (metabolic pathways) of uncharacterized enzymes discovered in microbial genome projects using the ligand specificities of the solute binding proteins (SBPs) for ABC transporters. Using differential scanning fluorimetry, we determined that the SBP for an ABC transporter encoded by the genome of Mycobacterium smegmatis is stabilized by d-threitol. Using sequence similarity networks and genome neighborhood networks to guide selection of target proteins for pathway enzymes, we applied both in vitro and in vivo experimental approaches to discover novel pathways for catabolism of d-threitol, l-threitol, and erythritol.
		+
		+	A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis.,Huang H, Carter MS, Vetting MW, Al-Obaidi N, Patskovsky Y, Almo SC, Gerlt JA J Am Chem Soc. 2015 Nov 25;137(46):14570-3. doi: 10.1021/jacs.5b08968. Epub 2015 , Nov 12. PMID:26560079<ref>PMID:26560079</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4rs3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:37, 31 December 2014

OCA — Wed, 31 Dec 2014 09:37:16 GMT

←Older revision		Revision as of 09:37, 31 December 2014
Line 19:		Line 19:
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]
	[[Category: Glenn, A Scott]]		[[Category: Glenn, A Scott]]
-	[[Category: Hillerich, ~~R D~~]]	+	[[Category: Hillerich, B]]
	[[Category: Lafleur, J]]		[[Category: Lafleur, J]]
	[[Category: Love, J]]		[[Category: Love, J]]
Line 25:		Line 25:
	[[Category: Obaidi, N Al]]		[[Category: Obaidi, N Al]]
	[[Category: Patskovsky, Y]]		[[Category: Patskovsky, Y]]
-	[[Category: ~~Siede~~, B]]	+	[[Category: Siedel, R D]]
	[[Category: Toro, R]]		[[Category: Toro, R]]
	[[Category: Wasserman, S R]]		[[Category: Wasserman, S R]]

OCA: Protected "4rs3" [edit=sysop:move=sysop]

OCA — Wed, 19 Nov 2014 12:57:48 GMT

Protected "4rs3" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:57, 19 November 2014

OCA: New page: ==Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol==
OCA — Wed, 19 Nov 2014 12:57:45 GMT

New page: ==Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol== <StructureSection load='4rs3' size='340' side...

New page
==Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol==
<StructureSection load='4rs3' size='340' side='right' caption='[[4rs3]], [[Resolution|resolution]] 1.40Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4rs3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS3 OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS3 FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl">[[Non-Standard_Residue|NonStd Res:]]</td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Monosaccharide-transporting_ATPase Monosaccharide-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.17 3.6.3.17] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4rs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rs3 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs3 PDBsum]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Monosaccharide-transporting ATPase]]
[[Category: Almo, S C]]
[[Category: Attonito, J D]]
[[Category: Bhosle, R]]
[[Category: Chamala, S]]
[[Category: Chowdhury, S]]
[[Category: Efi, Enzyme Function Initiative]]
[[Category: Gerlt, J A]]
[[Category: Glenn, A Scott]]
[[Category: Hillerich, R D]]
[[Category: Lafleur, J]]
[[Category: Love, J]]
[[Category: Morisco, L L]]
[[Category: Obaidi, N Al]]
[[Category: Patskovsky, Y]]
[[Category: Siede, B]]
[[Category: Toro, R]]
[[Category: Wasserman, S R]]
[[Category: Whalen, K L]]
[[Category: Abc-type]]
[[Category: Efi]]
[[Category: Enzyme function initiative]]
[[Category: Hydrolase]]
[[Category: Structural genomic]]
[[Category: Sugar transporter]]
[[Category: Transport protein]]