OCA at 14:39, 29 November 2023

2023-11-29T14:39:28Z

←Older revision		Revision as of 14:39, 29 November 2023
Line 1:		Line 1:

	==Crystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate==		==Crystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate==
-	<StructureSection load='6loo' size='340' side='right'caption='[[6loo]]' scene=''>	+	<StructureSection load='6loo' size='340' side='right'caption='[[6loo]], [[Resolution\|resolution]] 1.99Å' 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=6LOO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LOO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6loo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_alcalophilus_ATCC_27647_=_CGMCC_1.3604 Alkalihalobacillus alcalophilus ATCC 27647 = CGMCC 1.3604]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LOO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LOO FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6loo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6loo OCA], [~~http~~://pdbe.org/6loo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6loo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6loo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6loo ProSAT]</span></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]] 1.99Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ELR:phosphono+[(3~{S},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl]+hydrogen+phosphate'>ELR</scene>, <scene name='pdbligand=ELU:phosphono+[(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl]+hydrogen+phosphate'>ELU</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=6loo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6loo OCA], [https://pdbe.org/6loo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6loo RCSB], [https://www.ebi.ac.uk/pdbsum/6loo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6loo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A094YZ24_ALKAL A0A094YZ24_ALKAL]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Terpene synthases (TS) are classified into two broad types, Class I and II, based on the chemical strategy for initial carbocation formation and motif sequences of the catalytic site. We have recently identified a new class of enzymes, Class IB, showing the acceptability of long (C20-C35) prenyl-diphosphates as substrates and no amino acid sequence homology with known TS. Conversion of long prenyl-diphosphates such as heptaprenyl-diphosphate (C35) is unusual and has never been reported for Class I and II enzymes. Therefore, the characterization of Class IB enzymes is crucial to understand the reaction mechanism of the extensive terpene synthesis. Here, we report the crystal structure bound with a substrate surrogate and biochemical analysis of a Class IB TS, using the enzyme from Bacillus alcalophilus (BalTS). The structure analysis revealed that the diphosphate part of the substrate is located around the two characteristic Asp-rich motifs, and the hydrophobic tail is accommodated in a unique hydrophobic long tunnel, where the C35 prenyl-diphosphate, the longest substrate of BalTS, can be accepted. Biochemical analyses of BalTS showed that the enzymatic property, such as Mg(2+) dependency, is similar to those of Class I enzymes. In addition, a new cyclic terpene was identified from BalTS reaction products. Mutational analysis revealed that five of the six Asp residues in the Asp-rich motifs and two His residues are essential for the formation of the cyclic skeleton. These results provided a clue to consider the application of the unusual large terpene synthesis by Class IB enzymes.
		+
		+	Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate.,Stepanova R, Inagi H, Sugawara K, Asada K, Nishi T, Ueda D, Yasuno Y, Shinada T, Miki K, Fujihashi M, Sato T ACS Chem Biol. 2020 Jun 19;15(6):1517-1525. doi: 10.1021/acschembio.0c00145. Epub, 2020 Apr 13. PMID:32227910<ref>PMID:32227910</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6loo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alkalihalobacillus alcalophilus ATCC 27647 = CGMCC 1 3604]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fujihashi M]]		[[Category: Fujihashi M]]
	[[Category: Inagi H]]		[[Category: Inagi H]]
	[[Category: Miki K]]		[[Category: Miki K]]

OCA at 09:31, 18 November 2020

2020-11-18T09:31:55Z

←Older revision		Revision as of 09:31, 18 November 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6loo is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate==
-		+	<StructureSection load='6loo' size='340' side='right'caption='[[6loo]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LOO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LOO FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6loo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6loo OCA], [http://pdbe.org/6loo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6loo RCSB], [http://www.ebi.ac.uk/pdbsum/6loo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6loo ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fujihashi M]]
		+	[[Category: Inagi H]]
		+	[[Category: Miki K]]

OCA at 13:00, 29 January 2020

2020-01-29T13:00:33Z

←Older revision		Revision as of 13:00, 29 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2020-01-22T13:33:53Z

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

←Older revision

Revision as of 13:33, 22 January 2020

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

2020-01-22T13:33:51Z

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

New page

'''Unreleased structure'''

The entry 6loo is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6loo - Revision history

OCA at 14:39, 29 November 2023

OCA at 09:31, 18 November 2020

OCA at 13:00, 29 January 2020

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

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