6dbz - Revision history

OCA at 14:33, 13 March 2024

OCA — Wed, 13 Mar 2024 14:33:43 GMT

←Older revision		Revision as of 14:33, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6dbz' size='340' side='right'caption='[[6dbz]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6dbz' size='340' side='right'caption='[[6dbz]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dbz]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dbz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DBZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=IPR:ISOPENTYL+PYROPHOSPHATE'>IPR</scene~~>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6dby\|6dby]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPR:ISOPENTYL+PYROPHOSPHATE'>IPR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">NUDT1, NUDX1, At1g68760, F14K14.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])~~</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=6dbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbz OCA], [https://pdbe.org/6dbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dbz RCSB], [https://www.ebi.ac.uk/pdbsum/6dbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbz 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=6dbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbz OCA], [~~http~~://pdbe.org/6dbz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dbz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dbz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NUDT1_ARATH NUDT1_ARATH]] Mediates the hydrolysis of some nucleoside diphosphate derivatives. Its substrate specificity is unclear. In vitro, it can use NTP, dNTP, 8-oxo-GTP, 8-oxo-dGTP, dGTP, dATP, dTTP or dihydroneopterin triphosphate (DHNTP) as substrate. Has some NADH pyrophosphatase activity in vitro; however, such activity may not be relevant in vivo due to the high concentration of manganese used during the experiments. Plays an important role in protection against oxidative DNA and RNA damage by removing oxidatively damaged form of guanine.<ref>PMID:15611104</ref> <ref>PMID:15878881</ref> <ref>PMID:17804481</ref>	+	[https://www.uniprot.org/uniprot/NUDT1_ARATH NUDT1_ARATH] Mediates the hydrolysis of some nucleoside diphosphate derivatives. Its substrate specificity is unclear. In vitro, it can use NTP, dNTP, 8-oxo-GTP, 8-oxo-dGTP, dGTP, dATP, dTTP or dihydroneopterin triphosphate (DHNTP) as substrate. Has some NADH pyrophosphatase activity in vitro; however, such activity may not be relevant in vivo due to the high concentration of manganese used during the experiments. Plays an important role in protection against oxidative DNA and RNA damage by removing oxidatively damaged form of guanine.<ref>PMID:15611104</ref> <ref>PMID:15878881</ref> <ref>PMID:17804481</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Plant genomes encode isopentenyl phosphate kinases (IPKs) that reactivate isopentenyl phosphate (IP) via ATP-dependent phosphorylation, forming the primary metabolite isopentenyl diphosphate (IPP) used generally for isoprenoid/terpenoid biosynthesis. Therefore, the existence of IPKs in plants raises unanswered questions concerning the origin and regulatory roles of IP in plant terpenoid metabolism. Here, we provide genetic and biochemical evidence showing that IP forms during specific dephosphorylation of IPP catalysed by a subset of Nudix superfamily hydrolases. Increasing metabolically available IP by overexpression of a bacterial phosphomevalonate decarboxylase (MPD) in Nicotiana tabacum resulted in significant enhancement in both monoterpene and sesquiterpene production. These results indicate that perturbing IP metabolism results in measurable changes in terpene products derived from both the methylerythritol phosphate (MEP) and mevalonate (MVA) pathways. Moreover, the unpredicted peroxisomal localization of bacterial MPD led us to discover that the step catalysed by phosphomevalonate kinase (PMK) imposes a hidden constraint on flux through the classical MVA pathway. These complementary findings fundamentally alter conventional views of metabolic regulation of terpenoid metabolism in plants and provide new metabolic engineering targets for the production of high-value terpenes in plants.	+
-		+
-	Contribution of isopentenyl phosphate to plant terpenoid metabolism.,Henry LK, Thomas ST, Widhalm JR, Lynch JH, Davis TC, Kessler SA, Bohlmann J, Noel JP, Dudareva N Nat Plants. 2018 Sep;4(9):721-729. doi: 10.1038/s41477-018-0220-z. Epub 2018 Aug , 20. PMID:30127411<ref>PMID:30127411</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6dbz" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
-	*[[~~Nudix hydrolase~~ 3D structures\|~~Nudix hydrolase~~ 3D structures]]	+	*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures\|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dudareva, N]]	+	[[Category: Dudareva N]]
-	[[Category: Henry~~, L K~~]]	+	[[Category: Henry LK]]
-	[[Category: Noel~~, J P~~]]	+	[[Category: Noel JP]]
-	[[Category: Thomas~~, S T]]~~	+	[[Category: Thomas ST]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phosphatase~~]]	+

OCA at 17:18, 20 November 2019

OCA — Wed, 20 Nov 2019 17:18:14 GMT

←Older revision		Revision as of 17:18, 20 November 2019
Line 1:		Line 1:

	==Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate==		==Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate==
-	<StructureSection load='6dbz' size='340' side='right' caption='[[6dbz]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6dbz' size='340' side='right'caption='[[6dbz]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dbz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dbz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPR:ISOPENTYL+PYROPHOSPHATE'>IPR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPR:ISOPENTYL+PYROPHOSPHATE'>IPR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[~~pdb~~\|~~pdb~~]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dby\|6dby]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NUDT1, NUDX1, At1g68760, F14K14.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=6dbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbz OCA], [http://pdbe.org/6dbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbz RCSB], [http://www.ebi.ac.uk/pdbsum/6dbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbz 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=6dbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbz OCA], [http://pdbe.org/6dbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbz RCSB], [http://www.ebi.ac.uk/pdbsum/6dbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbz ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6dbz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dbz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nudix hydrolase 3D structures\|Nudix hydrolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Dudareva, N]]		[[Category: Dudareva, N]]
	[[Category: Henry, L K]]		[[Category: Henry, L K]]

OCA at 19:49, 19 September 2018

OCA — Wed, 19 Sep 2018 19:49:22 GMT

←Older revision		Revision as of 19:49, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dbz is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate==
		+	<StructureSection load='6dbz' size='340' side='right' caption='[[6dbz]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dbz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPR:ISOPENTYL+PYROPHOSPHATE'>IPR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[pdb\|pdb]]</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=6dbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbz OCA], [http://pdbe.org/6dbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbz RCSB], [http://www.ebi.ac.uk/pdbsum/6dbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NUDT1_ARATH NUDT1_ARATH]] Mediates the hydrolysis of some nucleoside diphosphate derivatives. Its substrate specificity is unclear. In vitro, it can use NTP, dNTP, 8-oxo-GTP, 8-oxo-dGTP, dGTP, dATP, dTTP or dihydroneopterin triphosphate (DHNTP) as substrate. Has some NADH pyrophosphatase activity in vitro; however, such activity may not be relevant in vivo due to the high concentration of manganese used during the experiments. Plays an important role in protection against oxidative DNA and RNA damage by removing oxidatively damaged form of guanine.<ref>PMID:15611104</ref> <ref>PMID:15878881</ref> <ref>PMID:17804481</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant genomes encode isopentenyl phosphate kinases (IPKs) that reactivate isopentenyl phosphate (IP) via ATP-dependent phosphorylation, forming the primary metabolite isopentenyl diphosphate (IPP) used generally for isoprenoid/terpenoid biosynthesis. Therefore, the existence of IPKs in plants raises unanswered questions concerning the origin and regulatory roles of IP in plant terpenoid metabolism. Here, we provide genetic and biochemical evidence showing that IP forms during specific dephosphorylation of IPP catalysed by a subset of Nudix superfamily hydrolases. Increasing metabolically available IP by overexpression of a bacterial phosphomevalonate decarboxylase (MPD) in Nicotiana tabacum resulted in significant enhancement in both monoterpene and sesquiterpene production. These results indicate that perturbing IP metabolism results in measurable changes in terpene products derived from both the methylerythritol phosphate (MEP) and mevalonate (MVA) pathways. Moreover, the unpredicted peroxisomal localization of bacterial MPD led us to discover that the step catalysed by phosphomevalonate kinase (PMK) imposes a hidden constraint on flux through the classical MVA pathway. These complementary findings fundamentally alter conventional views of metabolic regulation of terpenoid metabolism in plants and provide new metabolic engineering targets for the production of high-value terpenes in plants.

-	~~Authors~~:	+	Contribution of isopentenyl phosphate to plant terpenoid metabolism.,Henry LK, Thomas ST, Widhalm JR, Lynch JH, Davis TC, Kessler SA, Bohlmann J, Noel JP, Dudareva N Nat Plants. 2018 Sep;4(9):721-729. doi: 10.1038/s41477-018-0220-z. Epub 2018 Aug , 20. PMID:30127411<ref>PMID:30127411</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6dbz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dudareva, N]]
		+	[[Category: Henry, L K]]
		+	[[Category: Noel, J P]]
		+	[[Category: Thomas, S T]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phosphatase]]

OCA at 04:03, 30 May 2018

OCA — Wed, 30 May 2018 04:03:09 GMT

←Older revision		Revision as of 04:03, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dbz is ON HOLD	+	The entry 6dbz is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6dbz" [edit=sysop:move=sysop]

OCA — Wed, 09 May 2018 04:59:20 GMT

Protected "6dbz" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:59, 9 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dbz is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 09 May 2018 04:59:19 GMT

New page: '''Unreleased structure''' The entry 6dbz is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6dbz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]