7w8x - Revision history

OCA at 17:37, 29 November 2023

OCA — Wed, 29 Nov 2023 17:37:56 GMT

←Older revision		Revision as of 17:37, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7w8x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._SN-593 Streptomyces sp. SN-593]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W8X FirstGlance]. <br>		<table><tr><td colspan='2'>[[7w8x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._SN-593 Streptomyces sp. SN-593]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W8X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8IK:(2S)-2-azanyl-3-(6-methyl-1H-indol-3-yl)propanoic+acid'>8IK</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.45Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8IK:(2S)-2-azanyl-3-(6-methyl-1H-indol-3-yl)propanoic+acid'>8IK</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7w8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w8x OCA], [https://pdbe.org/7w8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w8x RCSB], [https://www.ebi.ac.uk/pdbsum/7w8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w8x 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=7w8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w8x OCA], [https://pdbe.org/7w8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w8x RCSB], [https://www.ebi.ac.uk/pdbsum/7w8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w8x ProSAT]</span></td></tr>
	</table>		</table>

OCA at 19:23, 19 October 2022

OCA — Wed, 19 Oct 2022 19:23:17 GMT

←Older revision		Revision as of 19:23, 19 October 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7w8x is ~~ON HOLD until Paper~~ Publication	+	==DMSPP- and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA==
		+	<StructureSection load='7w8x' size='340' side='right'caption='[[7w8x]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7w8x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._SN-593 Streptomyces sp. SN-593]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W8X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8IK:(2S)-2-azanyl-3-(6-methyl-1H-indol-3-yl)propanoic+acid'>8IK</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7w8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w8x OCA], [https://pdbe.org/7w8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w8x RCSB], [https://www.ebi.ac.uk/pdbsum/7w8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w8x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D6RT90_9ACTN D6RT90_9ACTN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dimethylallyltryptophan synthases (DMATSs) catalyze the prenyl transfer reaction from dimethylallyl pyrophosphate (DMAPP) to an indole ring. IptA, a member of the DMATS family, is involved in biosynthesis of 6-dimethylallylindole-3-carbaldehyde in Streptomyces sp. SN-593 and catalyzes the C6-prenylation of l-Trp. The enzyme exhibits prenyl acceptor promiscuity and can accept various Trp derivatives, as observed in several other DMATS family members. Although many crystal structures of DMATS have been determined to date, the structural basis of substrate promiscuity and the acceptance of alternatives to indole-containing natural substrates remain to be clarified. In this study, we determined the crystal structures of the ternary l-Trp derivative (5-methyl-, 6-methyl-, and Nalpha-methyl-l-Trp) -DMSPP (dimethylallyl S-thiolopyrophosphate; stable analog of DMAPP) -enzyme complex of IptA, in addition to the substrate-free IptA and ternary l-Trp-DMSPP-IptA complex crystal structures. The overall structure of IptA exhibited a typical ABBA-fold, which is commonly found in DMATS family members, while l-Trp and DMSPP are found in a tunnel located inside the ABBA barrel. The crystal structure of the ternary l-Trp-DMSPP-enzyme complex can explain the electrophilic substitution at the C6 atom of l-Trp, which is assisted by Glu84 and His294, as previously suggested for other DMATSs. Although l-Trp snugly fitted into the active site pocket and the unoccupied space around l-Trp is very limited in the l-Trp-DMSPP-IptA complex structure, the enzyme can accommodate 5-methyl- and 6-methyl-l-Trp by slight relocation of the substrate indole ring and adjacent side chain in the active site, resulting in a higher prenylation activity for 5-methyl-l-Trp and C7 prenylation of 6-methyl-l-Trp. Like many other DMATSs, IptA cannot utilize prenyl donors larger than DMAPP. To enlarge the prenyl donor-binding pocket, the W154A mutation was introduced. As expected, this mutant produced prenylated l-Trp from l-Trp and geranyl- and farnesyl pyrophosphate.

-	~~Authors~~: Suemune, H., ~~Nagano~~, S., ~~Tomoya, H~~.	+	Crystal structures of a 6-dimethylallyltryptophan synthase, IptA: Insights into substrate tolerance and enhancement of prenyltransferase activity.,Suemune H, Nishimura D, Mizutani K, Sato Y, Hino T, Takagi H, Shiozaki-Sato Y, Takahashi S, Nagano S Biochem Biophys Res Commun. 2022 Feb 19;593:144-150. doi:, 10.1016/j.bbrc.2022.01.018. Epub 2022 Jan 12. PMID:35074664<ref>PMID:35074664</ref>

-	~~Description: DMSPP~~-~~and 6~~-~~Me-Trp-bound dimethylallyl tryptophan synthase, IptA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Nagano, S]]	+	<div class="pdbe-citations 7w8x" style="background-color:#fffaf0;"></div>
-	[[Category: Suemune, H]]	+	== References ==
-	[[Category: Tomoya, H]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Streptomyces sp. SN-593]]
		+	[[Category: Nagano S]]
		+	[[Category: Suemune H]]
		+	[[Category: Tomoya H]]

OCA at 06:07, 19 January 2022

OCA — Wed, 19 Jan 2022 06:07:47 GMT

←Older revision		Revision as of 06:07, 19 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7w8x is ON HOLD	+	The entry 7w8x is ON HOLD until Paper Publication

	Authors: Suemune, H., Nagano, S., Tomoya, H.		Authors: Suemune, H., Nagano, S., Tomoya, H.

OCA at 14:14, 22 December 2021

OCA — Wed, 22 Dec 2021 14:14:21 GMT

←Older revision		Revision as of 14:14, 22 December 2021
Line 3:		Line 3:
	The entry 7w8x is ON HOLD		The entry 7w8x is ON HOLD

-	Authors: ~~Hironori~~, S., ~~Shingo~~, N., Tomoya, H.	+	Authors: Suemune, H., Nagano, S., Tomoya, H.

	Description: DMSPP-and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA		Description: DMSPP-and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Hironori~~, S]]	+	[[Category: Nagano, S]]
-	[[Category: ~~Shingo~~, N]]	+	[[Category: Suemune, H]]
	[[Category: Tomoya, H]]		[[Category: Tomoya, H]]

OCA: Protected "7w8x" [edit=sysop:move=sysop]

OCA — Wed, 15 Dec 2021 15:51:31 GMT

Protected "7w8x" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:51, 15 December 2021

OCA: New page: '''Unreleased structure''' The entry 7w8x is ON HOLD Authors: Hironori, S., Shingo, N., Tomoya, H. Description: DMSPP-and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA [[Categ...

OCA — Wed, 15 Dec 2021 15:51:30 GMT

New page: '''Unreleased structure''' The entry 7w8x is ON HOLD Authors: Hironori, S., Shingo, N., Tomoya, H. Description: DMSPP-and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA [[Categ...

New page

'''Unreleased structure'''

The entry 7w8x is ON HOLD

Authors: Hironori, S., Shingo, N., Tomoya, H.

Description: DMSPP-and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA
[[Category: Unreleased Structures]]
[[Category: Hironori, S]]
[[Category: Shingo, N]]
[[Category: Tomoya, H]]