5ufn - Revision history

OCA at 14:26, 6 March 2024

OCA — Wed, 06 Mar 2024 14:26:56 GMT

←Older revision		Revision as of 14:26, 6 March 2024
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	<StructureSection load='5ufn' size='340' side='right'caption='[[5ufn]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='5ufn' size='340' side='right'caption='[[5ufn]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ufn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Burta Burta~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UFN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ufn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_thailandensis_E264 Burkholderia thailandensis E264]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UFN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.39Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ufm\|5ufm]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_II1283, DR63_4497 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 BURTA])</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=5ufn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ufn OCA], [https://pdbe.org/5ufn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ufn RCSB], [https://www.ebi.ac.uk/pdbsum/5ufn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ufn 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=5ufn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ufn OCA], [~~http~~://pdbe.org/5ufn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ufn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ufn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ufn ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q2T5S0_BURTA Q2T5S0_BURTA]
-	Burkholderia glumae converts the guanine base of guanosine triphosphate into an azapteridine and methylates both the pyrimidine and triazine rings to make toxoflavin. Strains of Burkholderia thailandensis and Burkholderia pseudomallei have a gene cluster encoding seven putative biosynthetic enzymes that resembles the toxoflavin gene cluster. Four of the enzymes are similar in sequence to BgToxBCDE, which have been proposed to make 1,6-didesmethyltoxoflavin (1,6-DDMT). One of the remaining enzymes, BthII1283 in B. thailandensis E264, is a predicted S-adenosylmethionine (SAM)-dependent N-methyltransferase that shows a low level of sequence identity to BgToxA, which sequentially methylates N6 and N1 of 1,6-DDMT to form toxoflavin. Here we show that, unlike BgToxA, BthII1283 catalyzes a single methyl transfer to N1 of 1,6-DDMT in vitro. In addition, we investigated the differences in reactivity and regioselectivity by determining crystal structures of BthII1283 with bound S-adenosylhomocysteine (SAH) or 1,6-DDMT and SAH. BthII1283 contains a class I methyltransferase fold and three unique extensions used for 1,6-DDMT recognition. The active site structure suggests that 1,6-DDMT is bound in a reduced form. The plane of the azapteridine ring system is orthogonal to its orientation in BgToxA. In BthII1283, the modeled SAM methyl group is directed toward the p orbital of N1, whereas in BgToxA, it is first directed toward an sp(2) orbital of N6 and then toward an sp(2) orbital of N1 after planar rotation of the azapteridine ring system. Furthermore, in BthII1283, N1 is hydrogen bonded to a histidine residue whereas BgToxA does not supply an obvious basic residue for either N6 or N1 methylation.	+
-		+
-	Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase.,Fenwick MK, Almabruk KH, Ealick SE, Begley TP, Philmus B Biochemistry. 2017 Aug 1;56(30):~~3934-3944. doi: 10.1021~~/~~acs.biochem.7b00476. Epub, 2017 Jul 20. PMID:28665591<ref>PMID:28665591<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5ufn" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burta~~]]	+	[[Category: Burkholderia thailandensis E264]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almabruk~~, K H~~]]	+	[[Category: Almabruk KH]]
-	[[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: Complex]]~~	+
-	~~[[Category: N-methyltransferase]]~~	+
-	~~[[Category: S-adenosylmethionine-dependent]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:29, 4 December 2019

OCA — Wed, 04 Dec 2019 09:29:07 GMT

←Older revision		Revision as of 09:29, 4 December 2019
Line 1:		Line 1:

	==Crystal structure of Burkholderia thailandensis 1,6-didemethyltoxoflavin-N1-methyltransferase with bound S-adenosylhomocysteine==		==Crystal structure of Burkholderia thailandensis 1,6-didemethyltoxoflavin-N1-methyltransferase with bound S-adenosylhomocysteine==
-	<StructureSection load='5ufn' size='340' side='right' caption='[[5ufn]], [[Resolution\|resolution]] 1.39Å' scene=''>	+	<StructureSection load='5ufn' size='340' side='right'caption='[[5ufn]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ufn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burta Burta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UFN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ufn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burta Burta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UFN FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Burta]]		[[Category: Burta]]
		+	[[Category: Large Structures]]
	[[Category: Almabruk, K H]]		[[Category: Almabruk, K H]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 08:30, 26 December 2018

OCA — Wed, 26 Dec 2018 08:30:06 GMT

←Older revision		Revision as of 08:30, 26 December 2018
Line 3:		Line 3:
	<StructureSection load='5ufn' size='340' side='right' caption='[[5ufn]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='5ufn' size='340' side='right' caption='[[5ufn]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ufn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ufn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burta Burta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UFN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ufm\|5ufm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ufm\|5ufm]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_II1283, DR63_4497 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 BURTA])</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=5ufn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ufn OCA], [http://pdbe.org/5ufn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ufn RCSB], [http://www.ebi.ac.uk/pdbsum/5ufn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ufn 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=5ufn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ufn OCA], [http://pdbe.org/5ufn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ufn RCSB], [http://www.ebi.ac.uk/pdbsum/5ufn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ufn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Burkholderia glumae converts the guanine base of guanosine triphosphate into an azapteridine and methylates both the pyrimidine and triazine rings to make toxoflavin. Strains of Burkholderia thailandensis and Burkholderia pseudomallei have a gene cluster encoding seven putative biosynthetic enzymes that resembles the toxoflavin gene cluster. Four of the enzymes are similar in sequence to BgToxBCDE, which have been proposed to make 1,6-didesmethyltoxoflavin (1,6-DDMT). One of the remaining enzymes, BthII1283 in B. thailandensis E264, is a predicted S-adenosylmethionine (SAM)-dependent N-methyltransferase that shows a low level of sequence identity to BgToxA, which sequentially methylates N6 and N1 of 1,6-DDMT to form toxoflavin. Here we show that, unlike BgToxA, BthII1283 catalyzes a single methyl transfer to N1 of 1,6-DDMT in vitro. In addition, we investigated the differences in reactivity and regioselectivity by determining crystal structures of BthII1283 with bound S-adenosylhomocysteine (SAH) or 1,6-DDMT and SAH. BthII1283 contains a class I methyltransferase fold and three unique extensions used for 1,6-DDMT recognition. The active site structure suggests that 1,6-DDMT is bound in a reduced form. The plane of the azapteridine ring system is orthogonal to its orientation in BgToxA. In BthII1283, the modeled SAM methyl group is directed toward the p orbital of N1, whereas in BgToxA, it is first directed toward an sp(2) orbital of N6 and then toward an sp(2) orbital of N1 after planar rotation of the azapteridine ring system. Furthermore, in BthII1283, N1 is hydrogen bonded to a histidine residue whereas BgToxA does not supply an obvious basic residue for either N6 or N1 methylation.
		+
		+	Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase.,Fenwick MK, Almabruk KH, Ealick SE, Begley TP, Philmus B Biochemistry. 2017 Aug 1;56(30):3934-3944. doi: 10.1021/acs.biochem.7b00476. Epub, 2017 Jul 20. PMID:28665591<ref>PMID:28665591</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ufn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Burta]]
	[[Category: Almabruk, K H]]		[[Category: Almabruk, K H]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 06:57, 13 December 2017

OCA — Wed, 13 Dec 2017 06:57:45 GMT

←Older revision		Revision as of 06:57, 13 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ufn is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Burkholderia thailandensis 1,6-didemethyltoxoflavin-N1-methyltransferase with bound S-adenosylhomocysteine==
-		+	<StructureSection load='5ufn' size='340' side='right' caption='[[5ufn]], [[Resolution\|resolution]] 1.39Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ufn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UFN FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ufm\|5ufm]]</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=5ufn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ufn OCA], [http://pdbe.org/5ufn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ufn RCSB], [http://www.ebi.ac.uk/pdbsum/5ufn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ufn ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Almabruk, K H]]
		+	[[Category: Begley, T P]]
		+	[[Category: Ealick, S E]]
		+	[[Category: Fenwick, M K]]
		+	[[Category: Philmus, B]]
		+	[[Category: Complex]]
		+	[[Category: N-methyltransferase]]
		+	[[Category: S-adenosylmethionine-dependent]]
		+	[[Category: Transferase]]

OCA at 14:25, 9 March 2017

OCA — Thu, 09 Mar 2017 14:25:37 GMT

←Older revision		Revision as of 14:25, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ufn is ON HOLD	+	The entry 5ufn is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 18 Jan 2017 14:51:02 GMT

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

←Older revision

Revision as of 14:51, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ufn is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Jan 2017 14:51:01 GMT

New page: '''Unreleased structure''' The entry 5ufn is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ufn is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]