6kd7 - Revision history

OCA at 10:30, 22 November 2023

2023-11-22T10:30:58Z

←Older revision		Revision as of 10:30, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6kd7' size='340' side='right'caption='[[6kd7]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6kd7' size='340' side='right'caption='[[6kd7]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kd7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Donghaeana_dokdonensis Donghaeana~~ dokdonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KD7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KD7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kd7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_dokdonensis_DSW-6 Nonlabens dokdonensis DSW-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KD7 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 2Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDD_1788 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=592029 Donghaeana dokdonensis])</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></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=6kd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kd7 OCA], [~~http~~://pdbe.org/6kd7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kd7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kd7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kd7 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=6kd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kd7 OCA], [https://pdbe.org/6kd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kd7 RCSB], [https://www.ebi.ac.uk/pdbsum/6kd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kd7 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/L7W5I6_NONDD L7W5I6_NONDD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6kd7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kd7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Geranylgeranyl pyrophosphate synthase 3D structures\|Geranylgeranyl pyrophosphate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Donghaeana dokdonensis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kim, K J~~]]	+	[[Category: Nonlabens dokdonensis DSW-6]]
-	[[Category: Kim~~, S~~]]	+	[[Category: Kim K-J]]
-	[[Category: ~~Prenyltransferase]]~~	+	[[Category: Kim S]]
-	~~[[Category: Transferase~~]]	+

OCA at 11:09, 2 October 2019

2019-10-02T11:09:01Z

←Older revision		Revision as of 11:09, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kd7 is ~~ON HOLD~~	+	==Crystal structure of geranylgeranyl pyrophosphate synthase==
		+	<StructureSection load='6kd7' size='340' side='right'caption='[[6kd7]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kd7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Donghaeana_dokdonensis Donghaeana dokdonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KD7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KD7 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDD_1788 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=592029 Donghaeana dokdonensis])</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=6kd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kd7 OCA], [http://pdbe.org/6kd7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kd7 RCSB], [http://www.ebi.ac.uk/pdbsum/6kd7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kd7 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isoprenoids comprise a diverse group of natural products with a broad range of metabolic functions. Isoprenoids are synthesized from prenyl pyrophosphates by prenyltransferases that catalyze the isoprenoid chain-elongation process to different chain lengths. We hereby present the crystal structure of geranylgeranyl pyrophosphate synthase from the marine flavobacterium Nonlabens dokdonensis DSW-6 (NdGGPPS). NdGGPPS forms a hexamer composed of homodimeric trimer, and the monomeric structure is composed of 15 alpha-helices (alpha1-alpha15). In this structure, we observed the binding of one pyrophosphate molecule and two glycerol molecules that mimicked substrate binding to the enzyme. The substrate binding site of NdGGPPS contains large hydrophobic residues such as Phe, His and Tyr, and structural and amino acids sequence analyses thereof suggest that the protein belongs to the short-chain prenyltransferase family.

-	~~Authors: Kim~~, S., Kim, K.-J.	+	Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6.,Kim S, Kim EJ, Park JB, Kim SW, Kim KJ Biochem Biophys Res Commun. 2019 Oct 20;518(3):479-485. doi:, 10.1016/j.bbrc.2019.08.071. Epub 2019 Aug 16. PMID:31427080<ref>PMID:31427080</ref>

-	~~Description: Crystal structure~~ of ~~geranylgeranyl pyrophosphate synthase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6kd7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Donghaeana dokdonensis]]
		+	[[Category: Large Structures]]
		+	[[Category: Kim, K J]]
	[[Category: Kim, S]]		[[Category: Kim, S]]
-	[[Category: ~~Kim, K.-J~~]]	+	[[Category: Prenyltransferase]]
		+	[[Category: Transferase]]

OCA: Protected "6kd7" [edit=sysop:move=sysop]

2019-07-10T03:59:26Z

Protected "6kd7" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:59, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kd7 is ON HOLD Authors: Kim, S., Kim, K.-J. Description: Crystal structure of geranylgeranyl pyrophosphate synthase [[Category: Unreleased Structu...

2019-07-10T03:59:25Z

New page: '''Unreleased structure''' The entry 6kd7 is ON HOLD Authors: Kim, S., Kim, K.-J. Description: Crystal structure of geranylgeranyl pyrophosphate synthase [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 6kd7 is ON HOLD

Authors: Kim, S., Kim, K.-J.

Description: Crystal structure of geranylgeranyl pyrophosphate synthase
[[Category: Unreleased Structures]]
[[Category: Kim, S]]
[[Category: Kim, K.-J]]