2isl - Revision history

OCA at 09:04, 21 February 2024

2024-02-21T09:04:19Z

← Older revision		Revision as of 09:04, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2isl' size='340' side='right'caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2isl' size='340' side='right'caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_9930 Atcc 9930~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 2.9Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2isj\|2isj]], [[2isk\|2isk]]</div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])~~</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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [https://pdbe.org/2isl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [https://www.ebi.ac.uk/pdbsum/2isl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isl 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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [https://pdbe.org/2isl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [https://www.ebi.ac.uk/pdbsum/2isl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/BLUB_RHIME BLUB_RHIME]] Involved in the biosynthesis of cobalamin (vitamin B12). Catalyzes the oxidative fragmentation and contraction of the isoalloxazine heterocycle and the cleavage of the ribityl tail of FMN(2) to form 5,6-dimethylbenzimidazole (DMB) and D-erythrose 4-phosphate (E4P). NAD(P)H is only required initially to reduce FMN and oxygen drives the oxidative fragmentation.<ref>PMID:16537439</ref> <ref>PMID:17377583</ref>		[https://www.uniprot.org/uniprot/BLUB_RHIME BLUB_RHIME] Involved in the biosynthesis of cobalamin (vitamin B12). Catalyzes the oxidative fragmentation and contraction of the isoalloxazine heterocycle and the cleavage of the ribityl tail of FMN(2) to form 5,6-dimethylbenzimidazole (DMB) and D-erythrose 4-phosphate (E4P). NAD(P)H is only required initially to reduce FMN and oxygen drives the oxidative fragmentation.<ref>PMID:16537439</ref> <ref>PMID:17377583</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2isl ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2isl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Vitamin B12 (cobalamin) is among the largest known non-polymeric natural products, and the only vitamin synthesized exclusively by microorganisms. The biosynthesis of the lower ligand of vitamin B(12), 5,6-dimethylbenzimidazole (DMB), is poorly understood. Recently, we discovered that a Sinorhizobium meliloti gene, bluB, is necessary for DMB biosynthesis. Here we show that BluB triggers the unprecedented fragmentation and contraction of the bound flavin mononucleotide cofactor and cleavage of the ribityl tail to form DMB and D-erythrose 4-phosphate. Our structural analysis shows that BluB resembles an NAD(P)H-flavin oxidoreductase, except that its unusually tight binding pocket accommodates flavin mononucleotide but not NAD(P)H. We characterize crystallographically an early intermediate along the reaction coordinate, revealing molecular oxygen poised over reduced flavin. Thus, BluB isolates and directs reduced flavin to activate molecular oxygen for its own cannibalization. This investigation of the biosynthesis of DMB provides clarification of an aspect of vitamin B12 that was otherwise incomplete, and may contribute to a better understanding of vitamin B12-related disease.

	~~BluB cannibalizes flavin to form the lower ligand of vitamin B12.,Taga ME, Larsen NA, Howard-Jones AR, Walsh CT, Walker GC Nature. 2007 Mar 22;446(7134):449-53. PMID:17377583<ref>PMID:17377583</ref>~~

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2isl" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Atcc 9930]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Howard-Jones~~, A R~~]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Larsen~~, N A~~]]		[[Category: Howard-Jones AR]]
	[[Category: Taga~~, M E~~]]		[[Category: Larsen NA]]
	[[Category: Walker~~, G C~~]]		[[Category: Taga ME]]
	[[Category: Walsh~~, C T]]~~		[[Category: Walker GC]]
	~~[[Category: Flavin]]~~		[[Category: Walsh CT]]
	~~[[Category: Flavin destructase]]~~
	~~[[Category: Flavoprotein]]~~
	~~[[Category: Molecular oxygen]]~~
	~~[[Category: Monooxygenase]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 11:21, 31 March 2021

2021-03-31T11:21:44Z

← Older revision		Revision as of 11:21, 31 March 2021
Line 1:		Line 1:

	==BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)==		==BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)==
	<StructureSection load='2isl' size='340' side='right' caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2isl' size='340' side='right'caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ISL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2isj\|2isj]], [[2isk\|2isk]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [~~http~~://pdbe.org/2isl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2isl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2isl 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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [https://pdbe.org/2isl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [https://www.ebi.ac.uk/pdbsum/2isl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/BLUB_RHIME BLUB_RHIME]] Involved in the biosynthesis of cobalamin (vitamin B12). Catalyzes the oxidative fragmentation and contraction of the isoalloxazine heterocycle and the cleavage of the ribityl tail of FMN(2) to form 5,6-dimethylbenzimidazole (DMB) and D-erythrose 4-phosphate (E4P). NAD(P)H is only required initially to reduce FMN and oxygen drives the oxidative fragmentation.<ref>PMID:16537439</ref> <ref>PMID:17377583</ref>		[[https://www.uniprot.org/uniprot/BLUB_RHIME BLUB_RHIME]] Involved in the biosynthesis of cobalamin (vitamin B12). Catalyzes the oxidative fragmentation and contraction of the isoalloxazine heterocycle and the cleavage of the ribityl tail of FMN(2) to form 5,6-dimethylbenzimidazole (DMB) and D-erythrose 4-phosphate (E4P). NAD(P)H is only required initially to reduce FMN and oxygen drives the oxidative fragmentation.<ref>PMID:16537439</ref> <ref>PMID:17377583</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 9930]]		[[Category: Atcc 9930]]
			[[Category: Large Structures]]
	[[Category: Howard-Jones, A R]]		[[Category: Howard-Jones, A R]]
	[[Category: Larsen, N A]]		[[Category: Larsen, N A]]

OCA at 08:38, 4 July 2018

2018-07-04T08:38:37Z

← Older revision		Revision as of 08:38, 4 July 2018
Line 1:		Line 1:

	==BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)==		==BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)==
	<StructureSection load='2isl' size='340' side='right' caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2isl' size='340' side='right' caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [http://pdbe.org/2isl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [http://www.ebi.ac.uk/pdbsum/2isl 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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [http://pdbe.org/2isl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [http://www.ebi.ac.uk/pdbsum/2isl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2isl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/is/2isl_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/is/2isl_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2isl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:35, 11 September 2015

2015-09-11T09:35:43Z

← Older revision		Revision as of 09:35, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2isl' size='340' side='right' caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2isl' size='340' side='right' caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sinorhizobium_meliloti Sinorhizobium meliloti~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ~~Sinorhizobium meliloti~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 ATCC 9930])</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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [http://www.ebi.ac.uk/pdbsum/2isl 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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [http://pdbe.org/2isl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [http://www.ebi.ac.uk/pdbsum/2isl PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/BLUB_RHIME BLUB_RHIME]] Involved in the biosynthesis of cobalamin (vitamin B12). Catalyzes the oxidative fragmentation and contraction of the isoalloxazine heterocycle and the cleavage of the ribityl tail of FMN(2) to form 5,6-dimethylbenzimidazole (DMB) and D-erythrose 4-phosphate (E4P). NAD(P)H is only required initially to reduce FMN and oxygen drives the oxidative fragmentation.<ref>PMID:16537439</ref> <ref>PMID:17377583</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 28:
	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 2isl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Sinorhizobium meliloti~~]]		[[Category: Atcc 9930]]
	[[Category: Howard-Jones, A R]]		[[Category: Howard-Jones, A R]]
	[[Category: Larsen, N A]]		[[Category: Larsen, N A]]

OCA at 08:43, 16 January 2015

2015-01-16T08:43:47Z

← Older revision		Revision as of 08:43, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISL FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [http://www.ebi.ac.uk/pdbsum/2isl 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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [http://www.ebi.ac.uk/pdbsum/2isl PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Howard-Jones, A R.]]		[[Category: Howard-Jones, A R]]
	[[Category: Larsen, N A.]]		[[Category: Larsen, N A]]
	[[Category: Taga, M E.]]		[[Category: Taga, M E]]
	[[Category: Walker, G C.]]		[[Category: Walker, G C]]
	[[Category: Walsh, C T.]]		[[Category: Walsh, C T]]
	[[Category: Flavin]]		[[Category: Flavin]]
	[[Category: Flavin destructase]]		[[Category: Flavin destructase]]

OCA at 10:17, 30 September 2014

2014-09-30T10:17:31Z

← Older revision		Revision as of 10:17, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2isl~~.~~png~~\|~~left~~\|~~200px~~]]		==BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)==
			<StructureSection load='2isl' size='340' side='right' caption='[[2isl]], [[Resolution\|resolution]] 2.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2isl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISL FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2isj\|2isj]], [[2isk\|2isk]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bluB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</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=2isl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isl RCSB], [http://www.ebi.ac.uk/pdbsum/2isl PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/is/2isl_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Vitamin B12 (cobalamin) is among the largest known non-polymeric natural products, and the only vitamin synthesized exclusively by microorganisms. The biosynthesis of the lower ligand of vitamin B(12), 5,6-dimethylbenzimidazole (DMB), is poorly understood. Recently, we discovered that a Sinorhizobium meliloti gene, bluB, is necessary for DMB biosynthesis. Here we show that BluB triggers the unprecedented fragmentation and contraction of the bound flavin mononucleotide cofactor and cleavage of the ribityl tail to form DMB and D-erythrose 4-phosphate. Our structural analysis shows that BluB resembles an NAD(P)H-flavin oxidoreductase, except that its unusually tight binding pocket accommodates flavin mononucleotide but not NAD(P)H. We characterize crystallographically an early intermediate along the reaction coordinate, revealing molecular oxygen poised over reduced flavin. Thus, BluB isolates and directs reduced flavin to activate molecular oxygen for its own cannibalization. This investigation of the biosynthesis of DMB provides clarification of an aspect of vitamin B12 that was otherwise incomplete, and may contribute to a better understanding of vitamin B12-related disease.

	~~{{STRUCTURE_2isl\| PDB=2isl \| SCENE= }}~~		BluB cannibalizes flavin to form the lower ligand of vitamin B12.,Taga ME, Larsen NA, Howard-Jones AR, Walsh CT, Walker GC Nature. 2007 Mar 22;446(7134):449-53. PMID:17377583<ref>PMID:17377583</ref>

	~~===BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17377583}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2isl]] is~~ a ~~8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017377583<~~/~~ref><ref group="xtra">PMID:016537439</ref~~><~~references group="xtra"~~/>
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Howard-Jones, A R.]]		[[Category: Howard-Jones, A R.]]

OCA at 13:20, 30 January 2013

2013-01-30T13:20:57Z

← Older revision		Revision as of 13:20, 30 January 2013
Line 1:		Line 1:
	[[Image:2isl.png\|left\|200px]]		[[Image:2isl.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2isl", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2isl\| PDB=2isl \| SCENE= }}		{{STRUCTURE_2isl\| PDB=2isl \| SCENE= }}

	===BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)===		===BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17377583}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17377583 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17377583}}		{{ABSTRACT_PUBMED_17377583}}

Line 22:		Line 11:

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17377583~~</ref><ref group="xtra">PMID:~~16537439~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017377583</ref><ref group="xtra">PMID:016537439</ref><references group="xtra"/>
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Howard-Jones, A R.]]		[[Category: Howard-Jones, A R.]]

OCA: Protected "2isl" [edit=sysop:move=sysop]

2011-03-14T22:57:32Z

Protected "2isl" [edit=sysop:move=sysop]

← Older revision	Revision as of 22:57, 14 March 2011
(No difference)

OCA at 22:57, 14 March 2011

2011-03-14T22:57:30Z

← Older revision		Revision as of 22:57, 14 March 2011
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2isl.png\|left\|200px]]		[[Image:2isl.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
	~~2ISL~~ is a 8 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA].		[[2isl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISL OCA].

	==Reference==		==Reference==
Line 36:		Line 35:
	[[Category: Monooxygenase]]		[[Category: Monooxygenase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:35:54 2009''~~

OCA at 09:35, 22 March 2009

2009-03-22T09:35:54Z

← Older revision		Revision as of 09:35, 22 March 2009
Line 12:		Line 12:
	===BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)===		===BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)===


			<!--
			The line below this paragraph, {{ABSTRACT_PUBMED_17377583}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 17377583 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_17377583}}

	==About this Structure==		==About this Structure==
Line 17:		Line 23:

	==Reference==		==Reference==
	<ref group="xtra">PMID:16537439</ref><references group="xtra"/>		<ref group="xtra">PMID:17377583</ref><ref group="xtra">PMID:16537439</ref><references group="xtra"/>
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Howard-Jones, A R.]]		[[Category: Howard-Jones, A R.]]
Line 26:		Line 32:
	[[Category: Flavin]]		[[Category: Flavin]]
	[[Category: Flavin destructase]]		[[Category: Flavin destructase]]
			[[Category: Flavoprotein]]
	[[Category: Molecular oxygen]]		[[Category: Molecular oxygen]]
	[[Category: Monooxygenase]]		[[Category: Monooxygenase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 18~~:50:36 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:35:54 2009''