5jbx - Revision history

OCA at 10:58, 6 September 2023

OCA — Wed, 06 Sep 2023 10:58:30 GMT

←Older revision		Revision as of 10:58, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5jbx' size='340' side='right'caption='[[5jbx]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='5jbx' size='340' side='right'caption='[[5jbx]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jbx]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myxxd Myxxd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JBX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JBX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jbx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Myxococcus_xanthus_DK_1622 Myxococcus xanthus DK 1622]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JBX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=COA:COENZYME+A'>COA</scene>~~, ~~<scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 1.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>crt, MXAN_3757 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~246197 MYXXD])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydratase 3-hydroxybutyryl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.55 4.2.1.55]~~ </~~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=5jbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jbx OCA], [https://pdbe.org/5jbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jbx RCSB], [https://www.ebi.ac.uk/pdbsum/5jbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jbx ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jbx OCA], [~~http~~://pdbe.org/5jbx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jbx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jbx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jbx ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q1D5Y4_MYXXD Q1D5Y4_MYXXD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3-hydroxybutyryl-CoA dehydratase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myxxd~~]]	+	[[Category: Myxococcus xanthus DK 1622]]
-	[[Category: Blankenfeldt, W]]	+	[[Category: Blankenfeldt W]]
-	[[Category: Bock, T]]	+	[[Category: Bock T]]
-	[[Category: Mueller, R]]	+	[[Category: Mueller R]]
-	[[Category: Reichelt, J]]	+	[[Category: Reichelt J]]
-	~~[[Category: Dehydratase]]~~	+
-	~~[[Category: Isovalerate]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Myxococcus xanthus~~]]	+

OCA at 07:41, 10 June 2020

OCA — Wed, 10 Jun 2020 07:41:39 GMT

←Older revision		Revision as of 07:41, 10 June 2020
Line 1:		Line 1:

	==Crystal structure of LiuC in complex with coenzyme A and malonic acid==		==Crystal structure of LiuC in complex with coenzyme A and malonic acid==
-	<StructureSection load='5jbx' size='340' side='right' caption='[[5jbx]], [[Resolution\|resolution]] 1.10Å' scene=''>	+	<StructureSection load='5jbx' size='340' side='right'caption='[[5jbx]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jbx]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JBX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JBX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jbx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Myxxd Myxxd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JBX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JBX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">crt, MXAN_3757 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246197 MYXXD])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydratase 3-hydroxybutyryl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.55 4.2.1.55] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydratase 3-hydroxybutyryl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.55 4.2.1.55] </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=5jbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jbx OCA], [http://pdbe.org/5jbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jbx RCSB], [http://www.ebi.ac.uk/pdbsum/5jbx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jbx ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jbx OCA], [http://pdbe.org/5jbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jbx RCSB], [http://www.ebi.ac.uk/pdbsum/5jbx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jbx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: 3-hydroxybutyryl-CoA dehydratase]]		[[Category: 3-hydroxybutyryl-CoA dehydratase]]
		+	[[Category: Large Structures]]
		+	[[Category: Myxxd]]
	[[Category: Blankenfeldt, W]]		[[Category: Blankenfeldt, W]]
	[[Category: Bock, T]]		[[Category: Bock, T]]

OCA at 02:28, 13 July 2016

OCA — Wed, 13 Jul 2016 02:28:05 GMT

←Older revision		Revision as of 02:28, 13 July 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydratase 3-hydroxybutyryl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.55 4.2.1.55] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydratase 3-hydroxybutyryl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.55 4.2.1.55] </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=5jbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jbx OCA], [http://pdbe.org/5jbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jbx RCSB], [http://www.ebi.ac.uk/pdbsum/5jbx 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=5jbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jbx OCA], [http://pdbe.org/5jbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jbx RCSB], [http://www.ebi.ac.uk/pdbsum/5jbx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jbx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:09, 23 June 2016

OCA — Thu, 23 Jun 2016 23:09:24 GMT

←Older revision		Revision as of 23:09, 23 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jbx is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of LiuC in complex with coenzyme A and malonic acid==
		+	<StructureSection load='5jbx' size='340' side='right' caption='[[5jbx]], [[Resolution\|resolution]] 1.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jbx]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JBX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JBX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyryl-CoA_dehydratase 3-hydroxybutyryl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.55 4.2.1.55] </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=5jbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jbx OCA], [http://pdbe.org/5jbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jbx RCSB], [http://www.ebi.ac.uk/pdbsum/5jbx PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Myxobacteria are able to produce the important metabolite isovaleryl coenzyme A by using an alternative route besides leucine degradation. The first step into this pathway is mediated by LiuC, a member of the 3-methylglutaconyl CoA hydratases (MGCH). Here we present crystal structures refined to 2.05 A and 1.1 A of LiuC in the apo and the coenzyme A bound state, respectively. By using simulated annealing we modeled the enzyme substrate complex and identified residues potentially involved in substrate binding, specificity and catalysis. The dehydration of 3-hydroxy-3-methylglutaconyl CoA to 3-methylglutaconyl CoA catalyzed by LiuC involves Glu112 and Glu132 and likely proceeds via the typical crotonase acid-base mechanism. In this, Tyr231 and Arg69 are key players in positioning the substrate to enable proper catalysis. Surprisingly, LiuC shows higher sequence and structural similarity to human MGCH than to the bacterial form, although they convert the same substrate. This study provides structural insights into the alternative isovaleryl coenzyme A biosynthesis pathway and may open a gate for biofuel research, since isovaleryl CoA is a source for isobutene, a precursor for renewable fuels and chemicals.

-	~~Authors~~:	+	The structure of LiuC, a 3-hydroxy-3-methylglutaconyl CoA dehydratase involved in isovaleryl CoA biosynthesis in Myxococcus xanthus, reveals insights into specificity and catalysis.,Bock T, Reichelt J, Muller R, Blankenfeldt W Chembiochem. 2016 Jun 8. doi: 10.1002/cbic.201600225. PMID:27271456<ref>PMID:27271456</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jbx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 3-hydroxybutyryl-CoA dehydratase]]
		+	[[Category: Blankenfeldt, W]]
		+	[[Category: Bock, T]]
		+	[[Category: Mueller, R]]
		+	[[Category: Reichelt, J]]
		+	[[Category: Dehydratase]]
		+	[[Category: Isovalerate]]
		+	[[Category: Lyase]]
		+	[[Category: Myxococcus xanthus]]

OCA at 15:16, 15 May 2016

OCA — Sun, 15 May 2016 15:16:19 GMT

←Older revision		Revision as of 15:16, 15 May 2016
Line 3:		Line 3:
	The entry 5jbx is ON HOLD until Paper Publication		The entry 5jbx is ON HOLD until Paper Publication

-	Authors: ~~Bock, T., Reichelt, J., Mueller, R., Blankenfeldt, W.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Bock, T]]
-	[[Category: Mueller, R]]
-	[[Category: Blankenfeldt, W]]
-	[[Category: Reichelt, J]]

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

OCA — Wed, 11 May 2016 01:49:27 GMT

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

←Older revision

Revision as of 01:49, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jbx is ON HOLD until Paper Publication Authors: Bock, T., Reichelt, J., Mueller, R., Blankenfeldt, W. Description: [[Category: Unreleased Structu...

OCA — Wed, 11 May 2016 01:49:26 GMT

New page: '''Unreleased structure''' The entry 5jbx is ON HOLD until Paper Publication Authors: Bock, T., Reichelt, J., Mueller, R., Blankenfeldt, W. Description: [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5jbx is ON HOLD until Paper Publication

Authors: Bock, T., Reichelt, J., Mueller, R., Blankenfeldt, W.

Description:
[[Category: Unreleased Structures]]
[[Category: Bock, T]]
[[Category: Mueller, R]]
[[Category: Blankenfeldt, W]]
[[Category: Reichelt, J]]