5xk7 - Revision history

OCA at 08:05, 22 November 2023

OCA — Wed, 22 Nov 2023 08:05:10 GMT

←Older revision		Revision as of 08:05, 22 November 2023
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	==Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with DMAPP==		==Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with DMAPP==
-	<StructureSection load='5xk7' size='340' side='right' caption='[[5xk7]], [[Resolution\|resolution]] 1.91Å' scene=''>	+	<StructureSection load='5xk7' size='340' side='right'caption='[[5xk7]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xk7]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_sp.~~_cnh189~~ Streptomyces sp. ~~cnh189~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XK7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XK7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xk7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._CNH189 Streptomyces sp. CNH189]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XK7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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]] 1.911Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xk3\|5xk3]], [[5xk6\|5xk6]], [[5xk8\|5xk8]], [[5xk9\|5xk9]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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">mcl22 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1136432 Streptomyces sp. CNH189])</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=5xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xk7 OCA], [https://pdbe.org/5xk7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xk7 RCSB], [https://www.ebi.ac.uk/pdbsum/5xk7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xk7 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=5xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xk7 OCA], [~~http~~://pdbe.org/5xk7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xk7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xk7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xk7 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/M4T4U9_9ACTN M4T4U9_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5xk7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xk7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Undecaprenyl pyrophosphate synthase\|Undecaprenyl pyrophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces sp. ~~cnh189~~]]	+	[[Category: Large Structures]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Streptomyces sp. CNH189]]
-	[[Category: Gao, J]]	+	[[Category: Chen CC]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Gao J]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Guo RT]]
-	[[Category: Liu, W]]	+	[[Category: Ko TP]]
-	~~[[Category: Antibiotic biosynthesis]]~~	+	[[Category: Liu W]]
-	~~[[Category: Prenyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:18, 17 January 2018

OCA — Wed, 17 Jan 2018 08:18:37 GMT

←Older revision		Revision as of 08:18, 17 January 2018
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	<StructureSection load='5xk7' size='340' side='right' caption='[[5xk7]], [[Resolution\|resolution]] 1.91Å' scene=''>		<StructureSection load='5xk7' size='340' side='right' caption='[[5xk7]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xk7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XK7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XK7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xk7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp._cnh189 Streptomyces sp. cnh189]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XK7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XK7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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">[[5xk3\|5xk3]], [[5xk6\|5xk6]], [[5xk8\|5xk8]], [[5xk9\|5xk9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xk3\|5xk3]], [[5xk6\|5xk6]], [[5xk8\|5xk8]], [[5xk9\|5xk9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mcl22 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1136432 Streptomyces sp. CNH189])</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=5xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xk7 OCA], [http://pdbe.org/5xk7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xk7 RCSB], [http://www.ebi.ac.uk/pdbsum/5xk7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xk7 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=5xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xk7 OCA], [http://pdbe.org/5xk7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xk7 RCSB], [http://www.ebi.ac.uk/pdbsum/5xk7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xk7 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptomyces sp. cnh189]]
	[[Category: Chen, C C]]		[[Category: Chen, C C]]
	[[Category: Gao, J]]		[[Category: Gao, J]]

OCA at 08:29, 10 January 2018

OCA — Wed, 10 Jan 2018 08:29:13 GMT

←Older revision		Revision as of 08:29, 10 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xk7 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189 in complex with DMAPP==
		+	<StructureSection load='5xk7' size='340' side='right' caption='[[5xk7]], [[Resolution\|resolution]] 1.91Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xk7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XK7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XK7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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">[[5xk3\|5xk3]], [[5xk6\|5xk6]], [[5xk8\|5xk8]], [[5xk9\|5xk9]]</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=5xk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xk7 OCA], [http://pdbe.org/5xk7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xk7 RCSB], [http://www.ebi.ac.uk/pdbsum/5xk7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xk7 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report the first X-ray crystallographic structure of the "head-to-middle" prenyltransferase, isosesquilavandulyl diphosphate synthase, involved in biosynthesis of the merochlorin class of antibiotics. The protein adopts the zeta or cis-prenyl transferase fold but remarkably, unlike tuberculosinol adenosine synthase and other cis-prenyl transferases (e.g. cis-farnesyl, decaprenyl, undecaprenyl diphosphate synthases), the large, hydrophobic side chain does not occupy a central hydrophobic tunnel. Instead, it occupies a surface pocket oriented at 90 degrees to the hydrophobic tunnel. Product chain-length control is achieved by squeezing out the ligand from the conventional allylic S1 binding site, with proton abstraction being achieved using a diphosphate-Asn-Ser relay. The structures revise and unify our thinking as to the mechanism of action of many other prenyl transferases and may also be of use in engineering new merochlorin-class antibiotics.

-	~~Authors~~: Ko, ~~T.P.~~, ~~Guo~~, ~~R.T.~~, ~~Liu~~, W., Chen, C.C., ~~Gao, J~~.	+	"Head-to-Middle" and "Head-to-Tail" cis-Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase.,Gao J, Ko TP, Chen L, Malwal SR, Zhang J, Hu X, Qu F, Liu W, Huang JW, Cheng YS, Chen CC, Yang Y, Zhang Y, Oldfield E, Guo RT Angew Chem Int Ed Engl. 2018 Jan 15;57(3):683-687. doi: 10.1002/anie.201710185., Epub 2017 Dec 21. PMID:29215779<ref>PMID:29215779</ref>

-	~~Description: Structure~~ of ~~a prenyltransferase soaked with DMAPP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Ko, T.P]]~~	+	<div class="pdbe-citations 5xk7" style="background-color:#fffaf0;"></div>
-	~~[[Category: Liu, W]]~~	+	== References ==
-	[[Category: Chen, C.C]]	+	<references/>
-	~~[[Category: Guo, R.T~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, C C]]
	[[Category: Gao, J]]		[[Category: Gao, J]]
		+	[[Category: Guo, R T]]
		+	[[Category: Ko, T P]]
		+	[[Category: Liu, W]]
		+	[[Category: Antibiotic biosynthesis]]
		+	[[Category: Prenyltransferase]]
		+	[[Category: Transferase]]

OCA at 15:31, 27 September 2017

OCA — Wed, 27 Sep 2017 15:31:59 GMT

←Older revision		Revision as of 15:31, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xk7 is ON HOLD	+	The entry 5xk7 is ON HOLD until Paper Publication

	Authors: Ko, T.P., Guo, R.T., Liu, W., Chen, C.C., Gao, J.		Authors: Ko, T.P., Guo, R.T., Liu, W., Chen, C.C., Gao, J.
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	Description: Structure of a prenyltransferase soaked with DMAPP		Description: Structure of a prenyltransferase soaked with DMAPP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Ko, T.P]]
	[[Category: Liu, W]]		[[Category: Liu, W]]
	[[Category: Chen, C.C]]		[[Category: Chen, C.C]]
-	[[Category: Ko, T.P]]
	[[Category: Guo, R.T]]		[[Category: Guo, R.T]]
	[[Category: Gao, J]]		[[Category: Gao, J]]

OCA at 14:53, 17 May 2017

OCA — Wed, 17 May 2017 14:53:27 GMT

←Older revision		Revision as of 14:53, 17 May 2017
Line 3:		Line 3:
	The entry 5xk7 is ON HOLD		The entry 5xk7 is ON HOLD

-	Authors: ~~Tzu-Ping~~ Ko, ~~Rey-Ting~~ Guo, ~~Weidong~~ Liu, ~~Chun-Chi~~ Chen, ~~Jian~~ Gao	+	Authors: Ko, T.P., Guo, R.T., Liu, W., Chen, C.C., Gao, J.

-	Description: ~~structure~~ of a prenyltransferase soaked with DMAPP	+	Description: Structure of a prenyltransferase soaked with DMAPP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Tzu-Ping Ko, Rey-Ting Guo, Weidong~~ Liu, ~~Chun-Chi~~ Chen, ~~Jian~~ Gao]]	+	[[Category: Liu, W]]
		+	[[Category: Chen, C.C]]
		+	[[Category: Ko, T.P]]
		+	[[Category: Guo, R.T]]
		+	[[Category: Gao, J]]

OCA: Protected "5xk7" [edit=sysop:move=sysop]

OCA — Wed, 10 May 2017 12:03:20 GMT

Protected "5xk7" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:03, 10 May 2017

OCA: New page: '''Unreleased structure''' The entry 5xk7 is ON HOLD Authors: Tzu-Ping Ko, Rey-Ting Guo, Weidong Liu, Chun-Chi Chen, Jian Gao Description: structure of a prenyltransferase soaked with ...

OCA — Wed, 10 May 2017 12:03:19 GMT

New page: '''Unreleased structure''' The entry 5xk7 is ON HOLD Authors: Tzu-Ping Ko, Rey-Ting Guo, Weidong Liu, Chun-Chi Chen, Jian Gao Description: structure of a prenyltransferase soaked with ...

New page

'''Unreleased structure'''

The entry 5xk7 is ON HOLD

Authors: Tzu-Ping Ko, Rey-Ting Guo, Weidong Liu, Chun-Chi Chen, Jian Gao

Description: structure of a prenyltransferase soaked with DMAPP
[[Category: Unreleased Structures]]
[[Category: Tzu-Ping Ko, Rey-Ting Guo, Weidong Liu, Chun-Chi Chen, Jian Gao]]