2q1u - Revision history

OCA at 11:16, 30 August 2023

OCA — Wed, 30 Aug 2023 11:16:05 GMT

←Older revision		Revision as of 11:16, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2q1u' size='340' side='right'caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2q1u' size='340' side='right'caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"alcaligenes_bronchicanis"_(ferry_1911)_haupt_1935 "alcaligenes bronchicanis" (ferry 1911) haupt 1935~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow: auto; max-height~~: ~~3em;~~'>~~[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BbLPS1.16, wbmF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])~~</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [https://pdbe.org/2q1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [https://www.ebi.ac.uk/pdbsum/2q1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1u 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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [https://pdbe.org/2q1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [https://www.ebi.ac.uk/pdbsum/2q1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O87989_BORBO O87989_BORBO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bordetella bronchiseptica]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blundell~~, T L~~]]	+	[[Category: Blundell TL]]
-	[[Category: Harmer~~, N J~~]]	+	[[Category: Harmer NJ]]
-	[[Category: King~~, J D~~]]	+	[[Category: King JD]]
-	[[Category: Maskell, D]]	+	[[Category: Maskell D]]
-	[[Category: Palmer~~, C M]]~~	+	[[Category: Palmer CM]]
-	~~[[Category: Protein-nad+ complex]]~~	+
-	~~[[Category: Protein-udp complex]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 08:05, 25 June 2021

OCA — Fri, 25 Jun 2021 08:05:15 GMT

←Older revision		Revision as of 08:05, 25 June 2021
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	==Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP==		==Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP==
-	<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='2q1u' size='340' side='right'caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"alcaligenes_bronchicanis"_(ferry_1911)_haupt_1935 "alcaligenes bronchicanis" (ferry 1911) haupt 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"alcaligenes_bronchicanis"_(ferry_1911)_haupt_1935 "alcaligenes bronchicanis" (ferry 1911) haupt 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [~~http~~://pdbe.org/2q1u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2q1u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1u 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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [https://pdbe.org/2q1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [https://www.ebi.ac.uk/pdbsum/2q1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1u ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Blundell, T L]]		[[Category: Blundell, T L]]
	[[Category: Harmer, N J]]		[[Category: Harmer, N J]]

OCA at 08:34, 29 August 2018

OCA — Wed, 29 Aug 2018 08:34:14 GMT

←Older revision		Revision as of 08:34, 29 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP==		==Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP==
	<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://pdbe.org/2q1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u 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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://pdbe.org/2q1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1u ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1u_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1u_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>

OCA at 13:12, 9 February 2016

OCA — Tue, 09 Feb 2016 13:12:40 GMT

←Older revision		Revision as of 13:12, 9 February 2016
Line 16:		Line 16:
	<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=2q1u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:35, 10 September 2015

OCA — Thu, 10 Sep 2015 22:35:32 GMT

←Older revision		Revision as of 22:35, 10 September 2015
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u 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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://pdbe.org/2q1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2q1u" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:09, 25 January 2015

OCA — Sun, 25 Jan 2015 09:09:02 GMT

←Older revision		Revision as of 09:09, 25 January 2015
Line 2:		Line 2:
	<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"alcaligenes_bronchicanis"_(ferry_1911)_haupt_1935 "alcaligenes bronchicanis" (ferry 1911) haupt 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 "Alcaligenes bronchicanis" (Ferry 1911) Haupt 1935])</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u 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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u PDBsum]</span></td></tr>
	</table>		</table>

OCA at 07:20, 12 November 2014

OCA — Wed, 12 Nov 2014 07:20:29 GMT

←Older revision		Revision as of 07:20, 12 November 2014
Line 2:		Line 2:
	<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 Bordetella bronchiseptica])</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u 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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u PDBsum]</span></td></tr>
	</table>		</table>
Line 30:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Bordetella bronchiseptica]]~~	+	[[Category: Blundell, T L]]
-	[[Category: Blundell, T L.]]	+	[[Category: Harmer, N J]]
-	[[Category: Harmer, N J.]]	+	[[Category: King, J D]]
-	[[Category: King, J D.]]	+	[[Category: Maskell, D]]
-	[[Category: Maskell, D.]]	+	[[Category: Palmer, C M]]
-	[[Category: Palmer, C M.]]	+
	[[Category: Protein-nad+ complex]]		[[Category: Protein-nad+ complex]]
	[[Category: Protein-udp complex]]		[[Category: Protein-udp complex]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 14:22, 3 November 2014

OCA — Mon, 03 Nov 2014 14:22:51 GMT

OCA at 18:12, 30 September 2014

OCA — Tue, 30 Sep 2014 18:12:19 GMT

←Older revision		Revision as of 18:12, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2q1u.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP==
		+	<StructureSection load='2q1u' size='340' side='right' caption='[[2q1u]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 Bordetella bronchiseptica])</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u 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/q1/2q1u_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 ==
		+	The pathogenic bacteria Bordetella parapertussis and Bordetella bronchiseptica express a lipopolysaccharide O antigen containing a polymer of 2,3-diacetamido-2,3-dideoxy-l-galacturonic acid. The O-antigen cluster contains three neighbouring genes that encode proteins belonging to the short-chain dehydrogenase/reductase (SDR) family, wbmF, wbmG and wbmH, and we aimed to elucidate their individual functions. Mutation and complementation implicate each gene in O-antigen expression but, as their putative sugar nucleotide substrates are not currently available, biochemical characterisation of WbmF, WbmG and WbmH is impractical at the present time. SDR family members catalyse a wide range of chemical reactions including oxidation, reduction and epimerisation. Because they typically share low sequence conservation, however, catalytic function cannot be predicted from sequence analysis alone. In this context, structural characterisation of the native proteins, co-crystals and small-molecule soaks enables differentiation of the functions of WbmF, WbmG and WbmH. These proteins exhibit typical SDR architecture and coordinate NAD. In the substrate-binding domain, all three enzymes bind uridyl nucleotides. WbmG contains a typical SDR catalytic TYK triad, which is required for oxidoreductase function, but the active site is devoid of additional acid-base functionality. Similarly, WbmH possesses a TYK triad, but an otherwise feature-poor active site. Consequently, 3,5-epimerase function can probably be ruled out for these enzymes. The WbmF active site contains conserved 3,5-epimerase features, namely, a positionally conserved cysteine (Cys133) and basic side chain (His90 or Asn213), but lacks the serine/threonine component of the SDR triad and therefore may not act as an oxidoreductase. The data suggest a pathway for synthesis of the O-antigen precursor UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid and illustrate the usefulness of structural data in predicting protein function.

-	~~{{STRUCTURE_2q1u\| PDB=2q1u \| SCENE= }}~~	+	Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis.,King JD, Harmer NJ, Preston A, Palmer CM, Rejzek M, Field RA, Blundell TL, Maskell DJ J Mol Biol. 2007 Nov 30;374(3):749-63. Epub 2007 Sep 26. PMID:17950751<ref>PMID:17950751</ref>

-	~~===Crystal structure~~ of the ~~Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17950751}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2q1u]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017950751<~~/~~ref~~><~~ref group="xtra">PMID:017671375</ref><references group="xtra"~~/>	+
	[[Category: Bordetella bronchiseptica]]		[[Category: Bordetella bronchiseptica]]
	[[Category: Blundell, T L.]]		[[Category: Blundell, T L.]]

OCA at 13:19, 30 January 2013

OCA — Wed, 30 Jan 2013 13:19:52 GMT

←Older revision		Revision as of 13:19, 30 January 2013
Line 1:		Line 1:
	[[Image:2q1u.png\|left\|200px]]		[[Image:2q1u.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2q1u", 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_2q1u\| PDB=2q1u \| SCENE= }}		{{STRUCTURE_2q1u\| PDB=2q1u \| SCENE= }}

	===Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP===		===Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17950751}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17950751 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17950751}}		{{ABSTRACT_PUBMED_17950751}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17950751~~</ref><ref group="xtra">PMID:~~17671375~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017950751</ref><ref group="xtra">PMID:017671375</ref><references group="xtra"/>
	[[Category: Bordetella bronchiseptica]]		[[Category: Bordetella bronchiseptica]]
	[[Category: Blundell, T L.]]		[[Category: Blundell, T L.]]

←Older revision		Revision as of 14:22, 3 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q1u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1U FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pzj\|2pzj]], [[2q1s\|2q1s]], [[2q1t\|2q1t]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 Bordetella bronchiseptica])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BbLPS1.16, wbmF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518 Bordetella bronchiseptica])</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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u 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=2q1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1u RCSB], [http://www.ebi.ac.uk/pdbsum/2q1u 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 38:		Line 38:
	[[Category: Protein-nad+ complex]]		[[Category: Protein-nad+ complex]]
	[[Category: Protein-udp complex]]		[[Category: Protein-udp complex]]
-	[[Category: ~~Rossman~~ fold]]	+	[[Category: Rossmann fold]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]