7vpc - Revision history

OCA at 17:29, 29 November 2023

2023-11-29T17:29:44Z

←Older revision		Revision as of 17:29, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7vpc' size='340' side='right'caption='[[7vpc]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='7vpc' size='340' side='right'caption='[[7vpc]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7vpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VPC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vpc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VPC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=MLT:D-MALATE'>MLT</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]] 1.94Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/dimethylallylcistransferase dimethylallylcistransferase]~~, ~~with EC number [https~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.5.1.28 2.5.1.28]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene></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=7vpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vpc OCA], [https://pdbe.org/7vpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vpc RCSB], [https://www.ebi.ac.uk/pdbsum/7vpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vpc 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=7vpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vpc OCA], [https://pdbe.org/7vpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vpc RCSB], [https://www.ebi.ac.uk/pdbsum/7vpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vpc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CPT1_SOLLC CPT1_SOLLC]] Uses dimethylallyl diphosphate and isopentenyl diphosphate to catalyze the cis-prenyl chain elongation and produce the 10 carbon product neryl diphosphate.<ref>PMID:19487664</ref> <ref>PMID:23134568</ref> <ref>PMID:23757397</ref>	+	[https://www.uniprot.org/uniprot/CPT1_SOLLC CPT1_SOLLC] Uses dimethylallyl diphosphate and isopentenyl diphosphate to catalyze the cis-prenyl chain elongation and produce the 10 carbon product neryl diphosphate.<ref>PMID:19487664</ref> <ref>PMID:23134568</ref> <ref>PMID:23757397</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dimethylallylcistransferase~~]]	+	[[Category: Solanum lycopersicum]]
-	[[Category: Imaizumi, R]]	+	[[Category: Imaizumi R]]
-	[[Category: Kataoka, K]]	+	[[Category: Kataoka K]]
-	[[Category: Misawa, S]]	+	[[Category: Misawa S]]
-	[[Category: Nakayama, T]]	+	[[Category: Nakayama T]]
-	[[Category: Sakai, N]]	+	[[Category: Sakai N]]
-	[[Category: Takahashi, S]]	+	[[Category: Takahashi S]]
-	[[Category: Takeshita, K]]	+	[[Category: Takeshita K]]
-	[[Category: Yamamoto, M]]	+	[[Category: Yamamoto M]]
-	[[Category: Yamashita, S]]	+	[[Category: Yamashita S]]
-	~~[[Category: Isoprenoid]]~~	+
-	~~[[Category: Neryl diphosphate]]~~	+
-	~~[[Category: Plant protein]]~~	+
-	~~[[Category: Tomato]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:43, 18 August 2022

2022-08-18T06:43:54Z

←Older revision		Revision as of 06:43, 18 August 2022
Line 1:		Line 1:

	==Neryl diphosphate synthase from Solanum lycopersicum==		==Neryl diphosphate synthase from Solanum lycopersicum==
-	<StructureSection load='7vpc' size='340' side='right'caption='[[7vpc]]' scene=''>	+	<StructureSection load='7vpc' size='340' side='right'caption='[[7vpc]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VPC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vpc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VPC FirstGlance]. <br>
-	</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=7vpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vpc OCA], [https://pdbe.org/7vpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vpc RCSB], [https://www.ebi.ac.uk/pdbsum/7vpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vpc ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dimethylallylcistransferase dimethylallylcistransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.28 2.5.1.28] </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=7vpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vpc OCA], [https://pdbe.org/7vpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vpc RCSB], [https://www.ebi.ac.uk/pdbsum/7vpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vpc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CPT1_SOLLC CPT1_SOLLC]] Uses dimethylallyl diphosphate and isopentenyl diphosphate to catalyze the cis-prenyl chain elongation and produce the 10 carbon product neryl diphosphate.<ref>PMID:19487664</ref> <ref>PMID:23134568</ref> <ref>PMID:23757397</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most cis-prenyltransferases (cPTs) use all-trans-oligoprenyl diphosphate, such as (E,E)-farnesyl diphosphate (FPP, C15 ), but scarcely accept dimethylallyl diphosphate (DMAPP, C5 ), as an allylic diphosphate primer in consecutive cis-condensations of isopentenyl diphosphate. Consequently, naturally occurring cis-1,4-polyisoprenoids contain a few trans-isoprene units at their omega-end. However, some Solanum plants have distinct cPTs that primarily use DMAPP as a primer to synthesize all-cis-oligoprenyl diphosphates, such as neryl diphosphate (NPP, C10 ). However, the mechanism underlying the allylic substrate preference of cPTs remains unclear. In this study, we determined the crystal structure of NDPS1, an NPP synthase from tomato, and investigated critical residues for primer substrate preference through structural comparisons of cPTs. Highly conserved Gly and Trp in the primer substrate-binding region of cPTs were discovered to be substituted for Ile/Leu and Phe, respectively, in DMAPP-preferring cPTs. An I106G mutant of NDPS1 exhibited a low preference for DMAPP, but a higher preference for FPP. However, an I106G/F276W mutant preferred not only DMAPP but also all-trans-oligoprenyl diphosphates, with 15-fold higher catalytic efficiency than WT. Surprisingly, the mutant synthesized longer polyisoprenoids (~C50 ). Furthermore, one of the helix domains that constitute the hydrophobic cleft for accommodating elongating prenyl chains was also demonstrated to be critical in primer substrate preference. An NDPS1 I106G/F276W mutant with a chimeric helix domain swapped with that of a medium-chain cPT synthesizing C50-60 polyisoprenoids showed over 94-fold increase in catalytic efficiency for all primer substrates tested, resulting in longer products (~C70 ). These NDPS1 mutants could be used in the enzymatic synthesis of nonnatural all-cis-polyisoprenoids.
		+
		+	Structure-based engineering of a short-chain cis-prenyltransferase to biosynthesize nonnatural all-cis-polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain-length determination.,Kutsukawa R, Imaizumi R, Suenaga-Hiromori M, Takeshita K, Sakai N, Misawa S, Yamamoto M, Yamaguchi H, Miyagi-Inoue Y, Waki T, Kataoka K, Nakayama T, Yamashita S, Takahashi S FEBS J. 2022 Feb 8. doi: 10.1111/febs.16392. PMID:35133719<ref>PMID:35133719</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vpc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Imaizumi R]]	+	[[Category: Dimethylallylcistransferase]]
-	[[Category: Kataoka K]]	+	[[Category: Imaizumi, R]]
-	[[Category: Misawa S]]	+	[[Category: Kataoka, K]]
-	[[Category: Nakayama T]]	+	[[Category: Misawa, S]]
-	[[Category: Sakai N]]	+	[[Category: Nakayama, T]]
-	[[Category: Takahashi S]]	+	[[Category: Sakai, N]]
-	[[Category: Takeshita K]]	+	[[Category: Takahashi, S]]
-	[[Category: Yamamoto M]]	+	[[Category: Takeshita, K]]
-	[[Category: Yamashita S]]	+	[[Category: Yamamoto, M]]
		+	[[Category: Yamashita, S]]
		+	[[Category: Isoprenoid]]
		+	[[Category: Neryl diphosphate]]
		+	[[Category: Plant protein]]
		+	[[Category: Tomato]]
		+	[[Category: Transferase]]

OCA at 10:17, 18 May 2022

2022-05-18T10:17:48Z

←Older revision		Revision as of 10:17, 18 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7vpc ~~is ON HOLD until Paper Publication~~	+	==Neryl diphosphate synthase from Solanum lycopersicum==
-		+	<StructureSection load='7vpc' size='340' side='right'caption='[[7vpc]]' scene=''>
-	~~Authors~~: ~~Imaizumi, R~~.~~, Misawa, S~~.~~, Takeshita, K~~.~~, Sakai, N~~., ~~Yamamoto, M~~., ~~Kataoka, K~~., ~~Nakayama, T~~., ~~Takahashi, S~~., ~~Yamashita, S~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VPC FirstGlance]. <br>
-	~~Description: Neryl diphosphate synthase from Solanum lycopersicum~~	+	</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=7vpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vpc OCA], [https://pdbe.org/7vpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vpc RCSB], [https://www.ebi.ac.uk/pdbsum/7vpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vpc ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Misawa, S~~]]	+	__TOC__
-	[[Category: ~~Yamashita, S~~]]	+	</StructureSection>
-	[[Category: ~~Yamamoto, M~~]]	+	[[Category: Large Structures]]
-	[[Category: Nakayama, T]]	+	[[Category: Imaizumi R]]
-	[[Category: ~~Kataoka, K~~]]	+	[[Category: Kataoka K]]
-	[[Category: ~~Sakai, N~~]]	+	[[Category: Misawa S]]
-	[[Category: ~~Takahashi, S~~]]	+	[[Category: Nakayama T]]
-	[[Category: ~~Takeshita, K~~]]	+	[[Category: Sakai N]]
-	[[Category: ~~Imaizumi, R~~]]	+	[[Category: Takahashi S]]
		+	[[Category: Takeshita K]]
		+	[[Category: Yamamoto M]]
		+	[[Category: Yamashita S]]

OCA at 12:26, 29 December 2021

2021-12-29T12:26:33Z

←Older revision		Revision as of 12:26, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vpc is ON HOLD	+	The entry 7vpc is ON HOLD until Paper Publication

	Authors: Imaizumi, R., Misawa, S., Takeshita, K., Sakai, N., Yamamoto, M., Kataoka, K., Nakayama, T., Takahashi, S., Yamashita, S.		Authors: Imaizumi, R., Misawa, S., Takeshita, K., Sakai, N., Yamamoto, M., Kataoka, K., Nakayama, T., Takahashi, S., Yamashita, S.

OCA: Protected "7vpc" [edit=sysop:move=sysop]

2021-10-27T12:50:18Z

Protected "7vpc" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:50, 27 October 2021

OCA: New page: '''Unreleased structure''' The entry 7vpc is ON HOLD Authors: Imaizumi, R., Misawa, S., Takeshita, K., Sakai, N., Yamamoto, M., Kataoka, K., Nakayama, T., Takahashi, S., Yamashita, S. ...

2021-10-27T12:50:16Z

New page: '''Unreleased structure''' The entry 7vpc is ON HOLD Authors: Imaizumi, R., Misawa, S., Takeshita, K., Sakai, N., Yamamoto, M., Kataoka, K., Nakayama, T., Takahashi, S., Yamashita, S. ...

New page

'''Unreleased structure'''

The entry 7vpc is ON HOLD

Authors: Imaizumi, R., Misawa, S., Takeshita, K., Sakai, N., Yamamoto, M., Kataoka, K., Nakayama, T., Takahashi, S., Yamashita, S.

Description: Neryl diphosphate synthase from Solanum lycopersicum
[[Category: Unreleased Structures]]
[[Category: Misawa, S]]
[[Category: Yamashita, S]]
[[Category: Yamamoto, M]]
[[Category: Nakayama, T]]
[[Category: Kataoka, K]]
[[Category: Sakai, N]]
[[Category: Takahashi, S]]
[[Category: Takeshita, K]]
[[Category: Imaizumi, R]]