5je2 - Revision history

OCA at 12:37, 6 March 2024

2024-03-06T12:37:05Z

←Older revision		Revision as of 12:37, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q9LBJ0_BURGL Q9LBJ0_BURGL]		[https://www.uniprot.org/uniprot/Q9LBJ0_BURGL Q9LBJ0_BURGL]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Toxoflavin is a major virulence factor of the rice pathogen Burkholderia glumae. The tox operon of B. glumae contains five putative toxoflavin biosynthetic genes toxABCDE. ToxA is a predicted S-adenosylmethionine-dependent methyltransferase, and toxA knockouts of B. glumae are less virulent in plant infection models. In this study, we show that ToxA performs two consecutive methylations to convert the putative azapteridine intermediate, 1,6-didemethyltoxoflavin, to toxoflavin. In addition, we report a series of crystal structures of ToxA complexes that reveals the molecular basis of the dual methyltransferase activity. The results suggest sequential methylations with initial methylation at N6 of 1,6-didemethyltoxoflavin followed by methylation at N1. The two azapteridine orientations that position N6 or N1 for methylation are coplanar with a 140 degrees rotation between them. The structure of ToxA contains a class I methyltransferase fold having an N-terminal extension that either closes over the active site or is largely disordered. The ordered conformation places Tyr7 at a position of a structurally conserved tyrosine site of unknown function in various methyltransferases. Crystal structures of ToxA-Y7F consistently show a closed active site, whereas structures of ToxA-Y7A consistently show an open active site, suggesting that the hydroxyl group of Tyr7 plays a role in opening and closing the active site during the multistep reaction.
-
-	Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis.,Fenwick MK, Philmus B, Begley TP, Ealick SE Biochemistry. 2016 May 3. PMID:27070241<ref>PMID:27070241</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5je2" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:00, 6 September 2023

2023-09-06T11:00:45Z

←Older revision		Revision as of 11:00, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5je2' size='340' side='right'caption='[[5je2]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='5je2' size='340' side='right'caption='[[5je2]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5je2]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_33617 Atcc 33617~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JE2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JE2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5je2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_glumae Burkholderia glumae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JE2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.519Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5je6\|5je6]], [[5jdy\|5jdy]], [[5jdz\|5jdz]], [[5je0\|5je0]], [[5je1\|5je1]], [[5je3\|5je3]], [[5je4\|5je4]], [[5je5\|5je5]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">toxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=337 ATCC 33617])~~</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=5je2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5je2 OCA], [https://pdbe.org/5je2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5je2 RCSB], [https://www.ebi.ac.uk/pdbsum/5je2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5je2 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=5je2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5je2 OCA], [~~http~~://pdbe.org/5je2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5je2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5je2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5je2 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9LBJ0_BURGL Q9LBJ0_BURGL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 33617~~]]	+	[[Category: Burkholderia glumae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Begley~~, T P~~]]	+	[[Category: Begley TP]]
-	[[Category: Ealick~~, S E~~]]	+	[[Category: Ealick SE]]
-	[[Category: Fenwick~~, M K~~]]	+	[[Category: Fenwick MK]]
-	[[Category: Philmus, B]]	+	[[Category: Philmus B]]
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: N-methyltransferase]]~~	+
-	~~[[Category: Product complex]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:10, 4 December 2019

2019-12-04T09:10:01Z

←Older revision		Revision as of 09:10, 4 December 2019
Line 1:		Line 1:

	==Crystal structure of Burkholderia glumae ToxA Y7F mutant with bound S-adenosylhomocysteine (SAH)==		==Crystal structure of Burkholderia glumae ToxA Y7F mutant with bound S-adenosylhomocysteine (SAH)==
-	<StructureSection load='5je2' size='340' side='right' caption='[[5je2]], [[Resolution\|resolution]] 1.52Å' scene=''>	+	<StructureSection load='5je2' size='340' side='right'caption='[[5je2]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5je2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33617 Atcc 33617]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JE2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5je2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33617 Atcc 33617]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JE2 FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 33617]]		[[Category: Atcc 33617]]
		+	[[Category: Large Structures]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]
	[[Category: Ealick, S E]]		[[Category: Ealick, S E]]

OCA at 17:56, 15 November 2017

2017-11-15T17:56:05Z

←Older revision		Revision as of 17:56, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5je2' size='340' side='right' caption='[[5je2]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='5je2' size='340' side='right' caption='[[5je2]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5je2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JE2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5je2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33617 Atcc 33617]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JE2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5je6\|5je6]], [[5jdy\|5jdy]], [[5jdz\|5jdz]], [[5je0\|5je0]], [[5je1\|5je1]], [[5je3\|5je3]], [[5je4\|5je4]], [[5je5\|5je5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5je6\|5je6]], [[5jdy\|5jdy]], [[5jdz\|5jdz]], [[5je0\|5je0]], [[5je1\|5je1]], [[5je3\|5je3]], [[5je4\|5je4]], [[5je5\|5je5]]</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=5je2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5je2 OCA], [http://pdbe.org/5je2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5je2 RCSB], [http://www.ebi.ac.uk/pdbsum/5je2 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">toxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=337 ATCC 33617])</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=5je2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5je2 OCA], [http://pdbe.org/5je2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5je2 RCSB], [http://www.ebi.ac.uk/pdbsum/5je2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5je2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33617]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]
	[[Category: Ealick, S E]]		[[Category: Ealick, S E]]

OCA at 16:56, 15 May 2016

2016-05-15T16:56:59Z

←Older revision		Revision as of 16:56, 15 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5je2 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Burkholderia glumae ToxA Y7F mutant with bound S-adenosylhomocysteine (SAH)==
		+	<StructureSection load='5je2' size='340' side='right' caption='[[5je2]], [[Resolution\|resolution]] 1.52Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5je2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JE2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5je6\|5je6]], [[5jdy\|5jdy]], [[5jdz\|5jdz]], [[5je0\|5je0]], [[5je1\|5je1]], [[5je3\|5je3]], [[5je4\|5je4]], [[5je5\|5je5]]</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=5je2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5je2 OCA], [http://pdbe.org/5je2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5je2 RCSB], [http://www.ebi.ac.uk/pdbsum/5je2 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Toxoflavin is a major virulence factor of the rice pathogen Burkholderia glumae. The tox operon of B. glumae contains five putative toxoflavin biosynthetic genes toxABCDE. ToxA is a predicted S-adenosylmethionine-dependent methyltransferase, and toxA knockouts of B. glumae are less virulent in plant infection models. In this study, we show that ToxA performs two consecutive methylations to convert the putative azapteridine intermediate, 1,6-didemethyltoxoflavin, to toxoflavin. In addition, we report a series of crystal structures of ToxA complexes that reveals the molecular basis of the dual methyltransferase activity. The results suggest sequential methylations with initial methylation at N6 of 1,6-didemethyltoxoflavin followed by methylation at N1. The two azapteridine orientations that position N6 or N1 for methylation are coplanar with a 140 degrees rotation between them. The structure of ToxA contains a class I methyltransferase fold having an N-terminal extension that either closes over the active site or is largely disordered. The ordered conformation places Tyr7 at a position of a structurally conserved tyrosine site of unknown function in various methyltransferases. Crystal structures of ToxA-Y7F consistently show a closed active site, whereas structures of ToxA-Y7A consistently show an open active site, suggesting that the hydroxyl group of Tyr7 plays a role in opening and closing the active site during the multistep reaction.

-	~~Authors:~~ Fenwick~~, M.K.~~, Philmus, B., Begley~~, T.P.~~, Ealick~~, S~~.E.	+	Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis.,Fenwick MK, Philmus B, Begley TP, Ealick SE Biochemistry. 2016 May 3. PMID:27070241<ref>PMID:27070241</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Begley~~, ~~T.P~~]]	+	<div class="pdbe-citations 5je2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Begley, T P]]
		+	[[Category: Ealick, S E]]
		+	[[Category: Fenwick, M K]]
	[[Category: Philmus, B]]		[[Category: Philmus, B]]
-	[[Category: ~~Fenwick, M.K~~]]	+	[[Category: Mutant]]
-	[[Category: ~~Ealick, S.E~~]]	+	[[Category: N-methyltransferase]]
		+	[[Category: Product complex]]
		+	[[Category: Transferase]]

OCA: Protected "5je2" [edit=sysop:move=sysop]

2016-05-11T01:54:50Z

Protected "5je2" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:54, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5je2 is ON HOLD until Paper Publication Authors: Fenwick, M.K., Philmus, B., Begley, T.P., Ealick, S.E. Description: [[Category: Unreleased Struct...

2016-05-11T01:54:49Z

New page: '''Unreleased structure''' The entry 5je2 is ON HOLD until Paper Publication Authors: Fenwick, M.K., Philmus, B., Begley, T.P., Ealick, S.E. Description: [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 5je2 is ON HOLD until Paper Publication

Authors: Fenwick, M.K., Philmus, B., Begley, T.P., Ealick, S.E.

Description:
[[Category: Unreleased Structures]]
[[Category: Begley, T.P]]
[[Category: Philmus, B]]
[[Category: Fenwick, M.K]]
[[Category: Ealick, S.E]]