3wis - Revision history

OCA at 08:45, 20 March 2024

OCA — Wed, 20 Mar 2024 08:45:23 GMT

←Older revision		Revision as of 08:45, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3wis' size='340' side='right'caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3wis' size='340' side='right'caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Burkholderia_cepacia_lb400 Burkholderia cepacia lb400~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 1.901Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[4mwg\|4mwg]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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">Bxeno_B0583, Bxe_B2440, DmrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 Burkholderia cepacia LB400])~~</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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [https://pdbe.org/3wis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [https://www.ebi.ac.uk/pdbsum/3wis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wis 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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [https://pdbe.org/3wis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [https://www.ebi.ac.uk/pdbsum/3wis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wis ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q13QT8_PARXL Q13QT8_PARXL]
-	Dihydromethanopterin reductase (Dmr) is a redox enzyme that plays a key role in generating tetrahydromethanopterin (H4MPT) for use in one-carbon metabolism by archaea and some bacteria. DmrB is a bacterial enzyme understood to reduce dihydromethanopterin (H2MPT) to H4MPT using flavins as the source of reducing equivalents, but the mechanistic details have not been elucidated previously. Here we report the crystal structure of DmrB from Burkholderia xenovorans at a resolution of 1.9 A. Unexpectedly, the biological unit is a 24-mer composed of eight homotrimers located at the corners of a cubic cage-like structure. Within a homotrimer, each monomer-monomer interface exhibits an active site with two adjacently bound flavin mononucleotide (FMN) ligands, one deeply buried and tightly bound and one more peripheral, for a total of 48 ligands in the biological unit. Computational docking suggested that the peripheral site could bind either the observed FMN (the electron donor for the overall reaction) or the pterin, H2MPT (the electron acceptor for the overall reaction), in configurations ideal for electron transfer to and from the tightly bound FMN. On this basis, we propose that DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate. Sequence comparisons suggested that the catalytic mechanism is conserved among the bacterial homologs of DmrB and partially conserved in archaeal homologs, where an alternate electron donor is likely used. In addition to the mechanistic revelations, the structure of DmrB could help guide the development of anti-obesity drugs based on modification of the ecology of the human gut.	+
-		+
-	~~Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer.,McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA J Biol Chem. 2014 Mar 28;289(13)~~:~~8852-64. doi: 10.1074~~/~~jbc.M113.522342. Epub 2014, Feb 12. PMID:24523405<ref>PMID:24523405<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3wis" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Burkholderia cepacia lb400]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bobik~~, T A~~]]	+	[[Category: Paraburkholderia xenovorans LB400]]
-	[[Category: Bustos, C]]	+	[[Category: Bobik TA]]
-	[[Category: Cascio, D]]	+	[[Category: Bustos C]]
-	[[Category: Jorda, J]]	+	[[Category: Cascio D]]
-	[[Category: McNamara~~, D E~~]]	+	[[Category: Jorda J]]
-	[[Category: Rasche~~, M E~~]]	+	[[Category: McNamara DE]]
-	[[Category: Wang~~, T C~~]]	+	[[Category: Rasche ME]]
-	[[Category: Yeates~~, T O]]~~	+	[[Category: Wang TC]]
-	~~[[Category: Dihydromethanopterin reductase]]~~	+	[[Category: Yeates TO]]
-	~~[[Category: Flavin]]~~	+
-	~~[[Category: Methanopterin]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein cage~~]]	+

OCA at 05:38, 3 August 2022

OCA — Wed, 03 Aug 2022 05:38:02 GMT

←Older revision		Revision as of 05:38, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer==		==Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer==
-	<StructureSection load='3wis' size='340' side='right' caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3wis' size='340' side='right'caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WIS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WIS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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">[[4mwg\|4mwg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4mwg\|4mwg]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 Burkholderia cepacia LB400])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 Burkholderia cepacia LB400])</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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [~~http~~://pdbe.org/3wis PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wis PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wis 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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [https://pdbe.org/3wis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [https://www.ebi.ac.uk/pdbsum/3wis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wis ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Burkholderia cepacia lb400]]		[[Category: Burkholderia cepacia lb400]]
		+	[[Category: Large Structures]]
	[[Category: Bobik, T A]]		[[Category: Bobik, T A]]
	[[Category: Bustos, C]]		[[Category: Bustos, C]]

OCA at 08:07, 22 November 2017

OCA — Wed, 22 Nov 2017 08:07:08 GMT

←Older revision		Revision as of 08:07, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='3wis' size='340' side='right' caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3wis' size='340' side='right' caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burxl Burxl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WIS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WIS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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">[[4mwg\|4mwg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mwg\|4mwg]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 ~~BURXL~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 Burkholderia cepacia LB400])</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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [http://pdbe.org/3wis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [http://www.ebi.ac.uk/pdbsum/3wis PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wis 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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [http://pdbe.org/3wis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [http://www.ebi.ac.uk/pdbsum/3wis PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wis ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burxl~~]]	+	[[Category: Burkholderia cepacia lb400]]
	[[Category: Bobik, T A]]		[[Category: Bobik, T A]]
	[[Category: Bustos, C]]		[[Category: Bustos, C]]

OCA at 21:23, 11 August 2016

OCA — Thu, 11 Aug 2016 21:23:35 GMT

←Older revision		Revision as of 21:23, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer==		==Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer==
	<StructureSection load='3wis' size='340' side='right' caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3wis' size='340' side='right' caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mwg\|4mwg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mwg\|4mwg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [http://www.ebi.ac.uk/pdbsum/3wis 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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [http://pdbe.org/3wis PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [http://www.ebi.ac.uk/pdbsum/3wis PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wis ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3wis" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:07, 4 January 2015

OCA — Sun, 04 Jan 2015 11:07:27 GMT

←Older revision		Revision as of 11:07, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WIS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WIS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mwg\|4mwg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mwg\|4mwg]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [http://www.ebi.ac.uk/pdbsum/3wis 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=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [http://www.ebi.ac.uk/pdbsum/3wis PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer.,McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA J Biol Chem. 2014 Mar 28;289(13):8852-64. doi: 10.1074/jbc.M113.522342. Epub 2014, Feb 12. PMID:24523405<ref>PMID:24523405</ref>		Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer.,McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA J Biol Chem. 2014 Mar 28;289(13):8852-64. doi: 10.1074/jbc.M113.522342. Epub 2014, Feb 12. PMID:24523405<ref>PMID:24523405</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Burxl]]		[[Category: Burxl]]
-	[[Category: Bobik, T A.]]	+	[[Category: Bobik, T A]]
-	[[Category: Bustos, C.]]	+	[[Category: Bustos, C]]
-	[[Category: Cascio, D.]]	+	[[Category: Cascio, D]]
-	[[Category: Jorda, J.]]	+	[[Category: Jorda, J]]
-	[[Category: McNamara, D E.]]	+	[[Category: McNamara, D E]]
-	[[Category: Rasche, M E.]]	+	[[Category: Rasche, M E]]
-	[[Category: Wang, T C.]]	+	[[Category: Wang, T C]]
-	[[Category: Yeates, T O.]]	+	[[Category: Yeates, T O]]
	[[Category: Dihydromethanopterin reductase]]		[[Category: Dihydromethanopterin reductase]]
	[[Category: Flavin]]		[[Category: Flavin]]

OCA at 13:18, 18 May 2014

OCA — Sun, 18 May 2014 13:18:40 GMT

←Older revision		Revision as of 13:18, 18 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3wis\| PDB=3wis \| SCENE= }}~~	+	==Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer==
-	===Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer===	+	<StructureSection load='3wis' size='340' side='right' caption='[[3wis]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24523405}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wis]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WIS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mwg\|4mwg]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wis OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wis RCSB], [http://www.ebi.ac.uk/pdbsum/3wis PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dihydromethanopterin reductase (Dmr) is a redox enzyme that plays a key role in generating tetrahydromethanopterin (H4MPT) for use in one-carbon metabolism by archaea and some bacteria. DmrB is a bacterial enzyme understood to reduce dihydromethanopterin (H2MPT) to H4MPT using flavins as the source of reducing equivalents, but the mechanistic details have not been elucidated previously. Here we report the crystal structure of DmrB from Burkholderia xenovorans at a resolution of 1.9 A. Unexpectedly, the biological unit is a 24-mer composed of eight homotrimers located at the corners of a cubic cage-like structure. Within a homotrimer, each monomer-monomer interface exhibits an active site with two adjacently bound flavin mononucleotide (FMN) ligands, one deeply buried and tightly bound and one more peripheral, for a total of 48 ligands in the biological unit. Computational docking suggested that the peripheral site could bind either the observed FMN (the electron donor for the overall reaction) or the pterin, H2MPT (the electron acceptor for the overall reaction), in configurations ideal for electron transfer to and from the tightly bound FMN. On this basis, we propose that DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate. Sequence comparisons suggested that the catalytic mechanism is conserved among the bacterial homologs of DmrB and partially conserved in archaeal homologs, where an alternate electron donor is likely used. In addition to the mechanistic revelations, the structure of DmrB could help guide the development of anti-obesity drugs based on modification of the ecology of the human gut.

-	~~==About this~~ Structure==	+	Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer.,McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA J Biol Chem. 2014 Mar 28;289(13):8852-64. doi: 10.1074/jbc.M113.522342. Epub 2014, Feb 12. PMID:24523405<ref>PMID:24523405</ref>
-	~~[[3wis]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burxl Burxl]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3WIS OCA].~~	+

-	==~~Reference~~==	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024523405</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Burxl]]		[[Category: Burxl]]
	[[Category: Bobik, T A.]]		[[Category: Bobik, T A.]]

OCA at 06:49, 23 April 2014

OCA — Wed, 23 Apr 2014 06:49:04 GMT

←Older revision		Revision as of 06:49, 23 April 2014
Line 1:		Line 1:
	{{STRUCTURE_3wis\| PDB=3wis \| SCENE= }}		{{STRUCTURE_3wis\| PDB=3wis \| SCENE= }}
	===Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer===		===Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer===
		+	{{ABSTRACT_PUBMED_24523405}}

	==About this Structure==		==About this Structure==
-	[[3wis]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA].	+	[[3wis]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024523405</ref><references group="xtra"/><references/>
		+	[[Category: Burxl]]
	[[Category: Bobik, T A.]]		[[Category: Bobik, T A.]]
	[[Category: Bustos, C.]]		[[Category: Bustos, C.]]
	[[Category: Cascio, D.]]		[[Category: Cascio, D.]]
	[[Category: Jorda, J.]]		[[Category: Jorda, J.]]
-	[[Category: ~~Mcnamara~~, D E.]]	+	[[Category: McNamara, D E.]]
	[[Category: Rasche, M E.]]		[[Category: Rasche, M E.]]
	[[Category: Wang, T C.]]		[[Category: Wang, T C.]]

OCA at 17:41, 19 February 2014

OCA — Wed, 19 Feb 2014 17:41:52 GMT

←Older revision		Revision as of 17:41, 19 February 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3wis\| PDB=3wis \| SCENE= }}
		+	===Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer===

-	~~The entry~~ 3wis is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3wis]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WIS OCA].
-	~~Authors~~: Bobik, T.A., Cascio, D., Jorda, J., Mcnamara, D.E., ~~Bustos, C~~., Wang, T.C.~~, Rasche, M.E.,~~ Yeates, T.O.	+	[[Category: Bobik, T A.]]
-		+	[[Category: Bustos, C.]]
-	~~Description~~: ~~Crystal structure of Burkholderia xenovorans DmrB in complex with FMN~~: ~~A Cubic~~ Protein ~~Cage for Redox Transfer~~	+	[[Category: Cascio, D.]]
		+	[[Category: Jorda, J.]]
		+	[[Category: Mcnamara, D E.]]
		+	[[Category: Rasche, M E.]]
		+	[[Category: Wang, T C.]]
		+	[[Category: Yeates, T O.]]
		+	[[Category: Dihydromethanopterin reductase]]
		+	[[Category: Flavin]]
		+	[[Category: Methanopterin]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Protein cage]]

OCA: Protected "3wis" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2013 06:29:08 GMT

Protected "3wis" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:29, 2 October 2013

OCA: New page: '''Unreleased structure''' The entry 3wis is ON HOLD until Paper Publication Authors: Bobik, T.A., Cascio, D., Jorda, J., Mcnamara, D.E., Bustos, C., Wang, T.C., Rasche, M.E., Yeates, T...

OCA — Wed, 02 Oct 2013 06:29:07 GMT

New page: '''Unreleased structure''' The entry 3wis is ON HOLD until Paper Publication Authors: Bobik, T.A., Cascio, D., Jorda, J., Mcnamara, D.E., Bustos, C., Wang, T.C., Rasche, M.E., Yeates, T...

New page

'''Unreleased structure'''

The entry 3wis is ON HOLD until Paper Publication

Authors: Bobik, T.A., Cascio, D., Jorda, J., Mcnamara, D.E., Bustos, C., Wang, T.C., Rasche, M.E., Yeates, T.O.

Description: Crystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer