5ygk - Revision history

OCA at 08:29, 22 November 2023

2023-11-22T08:29:31Z

←Older revision		Revision as of 08:29, 22 November 2023
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	<StructureSection load='5ygk' size='340' side='right'caption='[[5ygk]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5ygk' size='340' side='right'caption='[[5ygk]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ygk]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strc1 Strc1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YGK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ygk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._CL190 Streptomyces sp. CL190]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YGK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</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]] 2.047Å</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=5ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygk OCA], [~~http~~://pdbe.org/5ygk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ygk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ygk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygk ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygk OCA], [https://pdbe.org/5ygk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ygk RCSB], [https://www.ebi.ac.uk/pdbsum/5ygk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/X5IYJ5_STRC1 X5IYJ5_STRC1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Strc1~~]]	+	[[Category: Streptomyces sp. CL190]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Chen CC]]
-	[[Category: Gao, J]]	+	[[Category: Gao J]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Guo RT]]
-	[[Category: Liu~~, W D]]~~	+	[[Category: Liu WD]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Cyclolavandulyl diphosphate synthase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Substrate binding~~]]	+

OCA at 12:42, 25 December 2019

2019-12-25T12:42:28Z

←Older revision		Revision as of 12:42, 25 December 2019
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	<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=5ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygk OCA], [http://pdbe.org/5ygk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygk RCSB], [http://www.ebi.ac.uk/pdbsum/5ygk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygk 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=5ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygk OCA], [http://pdbe.org/5ygk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygk RCSB], [http://www.ebi.ac.uk/pdbsum/5ygk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl diphosphate synthase containing two molecules of the substrate analog dimethylallyl (S)-thiolodiphosphate (DMASPP). The two molecules have similar diphosphate group orientations to those seen in other zeta-fold (cis- head-to-tail and head-to-middle) prenyltransferases with one diphosphate moiety forming a bidentate chelate with Mg(2+) in the so-called S1 site (which is typically the allylic binding site in zeta-fold proteins) while the second diphosphate binds to Mg(2+) in the so-called S2 site (which is typically the homoallylic binding site in zeta-fold proteins) via a single P1O1 oxygen. The latter interaction can facilitate direct phosphate-mediated proton abstraction via P1O2, or more likely by an indirect mechanism in which P1O2 stabilizes a basic asparagine species that removes H(+), which is then eliminated via an Asn-Ser shuttle. The universal occurrence of Asn-Ser pairs in zeta-fold proteins leads to the idea that the highly conserved amide (Asn, Gln) and OH-containing (Tyr) residues seen in many "head-to-head" prenyltransferases such as squalene and dehydrosqualene synthase might play similar roles, in H(+) elimination. Structural, bioinformatics and mutagenesis investigations indeed indicate an important role of these residues in catalysis, with the results of density functional theory calculations showing that Asn bound to Mg(2+) can act as a general (imine-like) base, while Gln, Tyr and H2O form a proton channel that is adjacent to the conventional (Asp-rich) "active site". Taken together, our results lead to mechanisms of proton-elimination from carbocations in numerous prenyltransferases in which neutral species (Asn, Gln, Ser, Tyr, H2O) act as proton shuttles, complementing the more familiar roles of acidic groups (in Asp and Glu) that bind to Mg(2+), and basic groups (primarily Arg) that bind to diphosphates, in isoprenoid biosynthesis.
		+
		+	Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.,Malwal SR, Gao J, Hu X, Yang Y, Liu W, Huang JW, Ko TP, Li L, Chen CC, O'Dowd B, Khade RL, Zhang Y, Zhang Y, Oldfield E, Guo RT ACS Catal. 2018 May 4;8(5):4299-4312. doi: 10.1021/acscatal.8b00543. Epub 2018, Apr 6. PMID:30345154<ref>PMID:30345154</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ygk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:00, 16 October 2019

2019-10-16T07:00:57Z

←Older revision		Revision as of 07:00, 16 October 2019
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	==Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp==		==Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp==
-	<StructureSection load='5ygk' size='340' side='right' caption='[[5ygk]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5ygk' size='340' side='right'caption='[[5ygk]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ygk]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ygk]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Strc1 Strc1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</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=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygk OCA], [http://pdbe.org/5ygk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygk RCSB], [http://www.ebi.ac.uk/pdbsum/5ygk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygk 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=5ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygk OCA], [http://pdbe.org/5ygk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygk RCSB], [http://www.ebi.ac.uk/pdbsum/5ygk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygk ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Strc1]]
	[[Category: Chen, C C]]		[[Category: Chen, C C]]
	[[Category: Gao, J]]		[[Category: Gao, J]]

OCA at 07:10, 25 July 2018

2018-07-25T07:10:32Z

←Older revision		Revision as of 07:10, 25 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5ygk is ON HOLD until Sep 23 2019~~	+	==Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp==
-		+	<StructureSection load='5ygk' size='340' side='right' caption='[[5ygk]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ygk]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGK FirstGlance]. <br>
-	~~Description:~~ Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ygk OCA], [http://pdbe.org/5ygk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ygk RCSB], [http://www.ebi.ac.uk/pdbsum/5ygk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ygk ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Liu~~, W.D]]	+	</table>
-	[[~~Category~~: ~~Chen~~, C.C]]	+	__TOC__
-	[[Category: ~~Guo~~, ~~R.T~~]]	+	</StructureSection>
		+	[[Category: Chen, C C]]
	[[Category: Gao, J]]		[[Category: Gao, J]]
		+	[[Category: Guo, R T]]
		+	[[Category: Liu, W D]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Cyclolavandulyl diphosphate synthase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Substrate binding]]

OCA at 05:35, 25 October 2017

2017-10-25T05:35:11Z

←Older revision		Revision as of 05:35, 25 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ygk is ON HOLD	+	The entry 5ygk is ON HOLD until Sep 23 2019

	Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.		Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.

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

2017-10-04T08:03:42Z

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

←Older revision

Revision as of 08:03, 4 October 2017

OCA: New page: '''Unreleased structure''' The entry 5ygk is ON HOLD Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T. Description: Crystal structure of a synthase from Streptomyces sp. CL190 with dm...

2017-10-04T08:03:40Z

New page: '''Unreleased structure''' The entry 5ygk is ON HOLD Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T. Description: Crystal structure of a synthase from Streptomyces sp. CL190 with dm...

New page

'''Unreleased structure'''

The entry 5ygk is ON HOLD

Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.

Description: Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp
[[Category: Unreleased Structures]]
[[Category: Liu, W.D]]
[[Category: Chen, C.C]]
[[Category: Guo, R.T]]
[[Category: Gao, J]]