5d01 - Revision history

OCA at 08:42, 27 September 2023

2023-09-27T08:42:03Z

←Older revision		Revision as of 08:42, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D01 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D01 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMT:(2S)-2-{[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}BUTANEDIOIC+ACID'>GMT</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]] 2.02Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMT:(2S)-2-{[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}BUTANEDIOIC+ACID'>GMT</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=5d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d01 OCA], [https://pdbe.org/5d01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d01 RCSB], [https://www.ebi.ac.uk/pdbsum/5d01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d01 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=5d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d01 OCA], [https://pdbe.org/5d01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d01 RCSB], [https://www.ebi.ac.uk/pdbsum/5d01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d01 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:16, 21 June 2023

2023-06-21T10:16:00Z

←Older revision		Revision as of 10:16, 21 June 2023
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	<StructureSection load='5d01' size='340' side='right'caption='[[5d01]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='5d01' size='340' side='right'caption='[[5d01]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D01 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D01 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GMT:(2S)-2-{[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}BUTANEDIOIC+ACID'>GMT</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMT:(2S)-2-{[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}BUTANEDIOIC+ACID'>GMT</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d00\|5d00]]</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=5d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d01 OCA], [https://pdbe.org/5d01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d01 RCSB], [https://www.ebi.ac.uk/pdbsum/5d01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d01 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bshA, jojH, ypjH, BSU22460 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d01 OCA], [~~http~~://pdbe.org/5d01 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d01 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d01 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d01 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BSHA_BACSU BSHA_BACSU]] Involved in bacillithiol (BSH) biosynthesis. Catalyzes the first step of the pathway, the formation of N-acetylglucosaminylmalate (GlcNAc-Mal) from UDP-N-acetylglucosamine (UDP-GlcNAc) and L-malate.<ref>PMID:20308541</ref> <ref>PMID:22569254</ref>	+	[https://www.uniprot.org/uniprot/BSHA_BACSU BSHA_BACSU] Involved in bacillithiol (BSH) biosynthesis. Catalyzes the first step of the pathway, the formation of N-acetylglucosaminylmalate (GlcNAc-Mal) from UDP-N-acetylglucosamine (UDP-GlcNAc) and L-malate.<ref>PMID:20308541</ref> <ref>PMID:22569254</ref>
	<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: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cook~~, P D~~]]	+	[[Category: Cook PD]]
-	[[Category: Winchell~~, K R]]~~	+	[[Category: Winchell KR]]
-	~~[[Category: Bacillithiol]]~~	+
-	~~[[Category: Glcnac]]~~	+
-	~~[[Category: Glycosyltransferase]]~~	+
-	~~[[Category: Gram-positive]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:00, 1 May 2019

2019-05-01T09:00:53Z

←Older revision		Revision as of 09:00, 1 May 2019
Line 1:		Line 1:

	==Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate==		==Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate==
-	<StructureSection load='5d01' size='340' side='right' caption='[[5d01]], [[Resolution\|resolution]] 2.02Å' scene=''>	+	<StructureSection load='5d01' size='340' side='right'caption='[[5d01]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D01 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D01 FirstGlance]. <br>
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BSHA_BACSU BSHA_BACSU]] Involved in bacillithiol (BSH) biosynthesis. Catalyzes the first step of the pathway, the formation of N-acetylglucosaminylmalate (GlcNAc-Mal) from UDP-N-acetylglucosamine (UDP-GlcNAc) and L-malate.<ref>PMID:20308541</ref> <ref>PMID:22569254</ref>		[[http://www.uniprot.org/uniprot/BSHA_BACSU BSHA_BACSU]] Involved in bacillithiol (BSH) biosynthesis. Catalyzes the first step of the pathway, the formation of N-acetylglucosaminylmalate (GlcNAc-Mal) from UDP-N-acetylglucosamine (UDP-GlcNAc) and L-malate.<ref>PMID:20308541</ref> <ref>PMID:22569254</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacillithiol is a compound produced by several Gram-positive bacterial species, including the human pathogens Staphylococcus aureus and Bacillus anthracis. It is involved in maintaining cellular redox balance as well as the destruction of reactive oxygen species and harmful xenobiotic agents, including the antibiotic fosfomycin. BshA, BshB, and BshC are the enzymes involved in bacillithiol biosynthesis. BshA is a retaining glycosyltransferase responsible for the first committed step in bacillithiol production, namely the addition of N-acetylglucosamine to l-malate. Retaining glycosyltransferases like BshA are proposed to utilize an SNi-like reaction mechanism in which leaving group departure and nucleophilic attack occur on the same face of the hexose. However, significant questions regarding the details of how BshA and similar enzymes accommodate their substrates and facilitate catalysis persist. Here we report X-ray crystallographic structures of BshA from Bacillus subtilis 168 bound with UMP and/or GlcNAc-mal at resolutions of 2.15 and 2.02 A, respectively. These ligand-bound structures, along with our functional and computational studies, provide clearer insight into how BshA and other retaining GT-B glycosyltransferases operate, corroborating the substrate-assisted, SNi-like reaction mechanism. The analyses presented herein can serve as the basis for the design of inhibitors capable of preventing bacillithiol production and, subsequently, help combat resistance to fosfomycin in various pathogenic Gram-positive microorganisms.
		+
		+	A Structural, Functional, and Computational Analysis of BshA, the First Enzyme in the Bacillithiol Biosynthesis Pathway.,Winchell KR, Egeler PW, VanDuinen AJ, Jackson LB, Karpen ME, Cook PD Biochemistry. 2016 Aug 23;55(33):4654-65. doi: 10.1021/acs.biochem.6b00472. Epub , 2016 Aug 11. PMID:27454321<ref>PMID:27454321</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5d01" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 16:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bacsu]]		[[Category: Bacsu]]
		+	[[Category: Large Structures]]
	[[Category: Cook, P D]]		[[Category: Cook, P D]]
	[[Category: Winchell, K R]]		[[Category: Winchell, K R]]

OCA at 12:29, 6 November 2017

2017-11-06T12:29:56Z

←Older revision		Revision as of 12:29, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5d01' size='340' side='right' caption='[[5d01]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='5d01' size='340' side='right' caption='[[5d01]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D01 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D01 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GMT:(2S)-2-{[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}BUTANEDIOIC+ACID'>GMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GMT:(2S)-2-{[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}BUTANEDIOIC+ACID'>GMT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d00\|5d00]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d00\|5d00]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bshA, jojH, ypjH, BSU22460 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d01 OCA], [http://pdbe.org/5d01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d01 RCSB], [http://www.ebi.ac.uk/pdbsum/5d01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d01 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=5d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d01 OCA], [http://pdbe.org/5d01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d01 RCSB], [http://www.ebi.ac.uk/pdbsum/5d01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d01 ProSAT]</span></td></tr>
	</table>		</table>
Line 14:		Line 15:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Cook, P D]]		[[Category: Cook, P D]]
	[[Category: Winchell, K R]]		[[Category: Winchell, K R]]

OCA at 21:01, 10 September 2016

2016-09-10T21:01:49Z

←Older revision		Revision as of 21:01, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5d01 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate==
-		+	<StructureSection load='5d01' size='340' side='right' caption='[[5d01]], [[Resolution\|resolution]] 2.02Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5d01]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D01 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GMT:(2S)-2-{[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}BUTANEDIOIC+ACID'>GMT</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d00\|5d00]]</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=5d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d01 OCA], [http://pdbe.org/5d01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d01 RCSB], [http://www.ebi.ac.uk/pdbsum/5d01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d01 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BSHA_BACSU BSHA_BACSU]] Involved in bacillithiol (BSH) biosynthesis. Catalyzes the first step of the pathway, the formation of N-acetylglucosaminylmalate (GlcNAc-Mal) from UDP-N-acetylglucosamine (UDP-GlcNAc) and L-malate.<ref>PMID:20308541</ref> <ref>PMID:22569254</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cook, P D]]
		+	[[Category: Winchell, K R]]
		+	[[Category: Bacillithiol]]
		+	[[Category: Glcnac]]
		+	[[Category: Glycosyltransferase]]
		+	[[Category: Gram-positive]]
		+	[[Category: Transferase]]

OCA at 11:41, 15 May 2016

2016-05-15T11:41:06Z

←Older revision		Revision as of 11:41, 15 May 2016
Line 3:		Line 3:
	The entry 5d01 is ON HOLD until Paper Publication		The entry 5d01 is ON HOLD until Paper Publication

-	Authors: ~~Cook, P.D., Winchell, K.R.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Cook, P.D]]
-	[[Category: Winchell, K.R]]

OCA at 10:49, 16 December 2015

2015-12-16T10:49:10Z

←Older revision		Revision as of 10:49, 16 December 2015
Line 7:		Line 7:
	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Winchell, K.R]]
	[[Category: Cook, P.D]]		[[Category: Cook, P.D]]
		+	[[Category: Winchell, K.R]]

OCA: Protected "5d01" [edit=sysop:move=sysop]

2015-08-12T13:38:38Z

Protected "5d01" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:38, 12 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d01 is ON HOLD until Paper Publication Authors: Cook, P.D., Winchell, K.R. Description: Category: Unreleased Structures [[Category: Winchell,...

2015-08-12T13:38:37Z

New page: '''Unreleased structure''' The entry 5d01 is ON HOLD until Paper Publication Authors: Cook, P.D., Winchell, K.R. Description: Category: Unreleased Structures [[Category: Winchell,...

New page

'''Unreleased structure'''

The entry 5d01 is ON HOLD until Paper Publication

Authors: Cook, P.D., Winchell, K.R.

Description:
[[Category: Unreleased Structures]]
[[Category: Winchell, K.R]]
[[Category: Cook, P.D]]