8db1 - Revision history

OCA at 07:25, 3 April 2024

2024-04-03T07:25:31Z

←Older revision		Revision as of 07:25, 3 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8db1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_fujikuroi Fusarium fujikuroi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8db1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_fujikuroi Fusarium fujikuroi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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]] 2.72Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=8db1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db1 OCA], [https://pdbe.org/8db1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db1 RCSB], [https://www.ebi.ac.uk/pdbsum/8db1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db1 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=8db1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db1 OCA], [https://pdbe.org/8db1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db1 RCSB], [https://www.ebi.ac.uk/pdbsum/8db1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DMAT1_GIBF5 DMAT1_GIBF5]] Dimethylallyltryptophan synthase; part of the DMATS1 gene cluster that mediates the biosynthesis of a reversely N-prenylated monomeric L-tryptophan (r-N-DMAT) (PubMed:28295904). The main product of the cluster is the r-N-DMAT produced by the dimethylallyltryptophan synthase DMATS1 and it remains unclear whether this metabolite undergoes further modifications when silent gene clusters are activated (PubMed:28295904). The acetylated form of r-N-DMAT, ac-r-N-DMAT, is also produced (PubMed:28295904). The roles of the cytochrome P450 monooxygenase FFUJ_09176 and the methyltransferase FFUJ_09178 have still to be elucidated (Probable).<ref>PMID:28295904</ref> <ref>PMID:28295904</ref>	+	[https://www.uniprot.org/uniprot/DMAT1_GIBF5 DMAT1_GIBF5] Dimethylallyltryptophan synthase; part of the DMATS1 gene cluster that mediates the biosynthesis of a reversely N-prenylated monomeric L-tryptophan (r-N-DMAT) (PubMed:28295904). The main product of the cluster is the r-N-DMAT produced by the dimethylallyltryptophan synthase DMATS1 and it remains unclear whether this metabolite undergoes further modifications when silent gene clusters are activated (PubMed:28295904). The acetylated form of r-N-DMAT, ac-r-N-DMAT, is also produced (PubMed:28295904). The roles of the cytochrome P450 monooxygenase FFUJ_09176 and the methyltransferase FFUJ_09178 have still to be elucidated (Probable).<ref>PMID:28295904</ref> <ref>PMID:28295904</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The regiospecific prenylation of an aromatic amino acid catalyzed by a dimethylallyl-l-tryptophan synthase (DMATS) is a key step in the biosynthesis of many fungal and bacterial natural products. DMATS enzymes share a common "ABBA" fold with divergent active site contours that direct alternative C-C, C-N, and C-O bond-forming trajectories. DMATS1 from Fusarium fujikuroi catalyzes the reverse N-prenylation of l-Trp by generating an allylic carbocation from dimethylallyl diphosphate (DMAPP) that then alkylates the indole nitrogen of l-Trp. DMATS1 stands out among the greater DMATS family because it exhibits unusually broad substrate specificity: it can utilize geranyl diphosphate (GPP) or l-Tyr as an alternative prenyl donor or acceptor, respectively; it can catalyze both forward and reverse prenylation, i.e., at C1 or C3 of DMAPP; and it can catalyze C-N and C-O bond-forming reactions. Here, we report the crystal structures of DMATS1 and its complexes with l-Trp or l-Tyr and unreactive thiolodiphosphate analogues of the prenyl donors DMAPP and GPP. Structures of ternary complexes mimic Michaelis complexes with actual substrates and illuminate active site features that govern prenylation regiochemistry. Comparison with CymD, a bacterial enzyme that catalyzes the reverse N-prenylation of l-Trp with DMAPP, indicates that bacterial and fungal DMATS enzymes share a conserved reaction mechanism. However, the narrower active site contour of CymD enforces narrower substrate specificity. Structure-function relationships established for DMATS enzymes will ultimately inform protein engineering experiments that will broaden the utility of these enzymes as useful tools for synthetic biology.	+
-		+
-	Structural Basis of Substrate Promiscuity and Catalysis by the Reverse Prenyltransferase N-Dimethylallyl-l-tryptophan Synthase from Fusarium fujikuroi.,Eaton SA, Ronnebaum TA, Roose BW, Christianson DW Biochemistry. 2022 Sep 20;61(18):2025-2035. doi: 10.1021/acs.biochem.2c00350., Epub 2022 Sep 9. PMID:36084241<ref>PMID:36084241</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 8db1" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:24, 28 September 2022

2022-09-28T06:24:01Z

←Older revision		Revision as of 06:24, 28 September 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 8db1 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of native DMATS1 prenyltransferase==
		+	<StructureSection load='8db1' size='340' side='right'caption='[[8db1]], [[Resolution\|resolution]] 2.72Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8db1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_fujikuroi Fusarium fujikuroi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=8db1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db1 OCA], [https://pdbe.org/8db1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db1 RCSB], [https://www.ebi.ac.uk/pdbsum/8db1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/DMAT1_GIBF5 DMAT1_GIBF5]] Dimethylallyltryptophan synthase; part of the DMATS1 gene cluster that mediates the biosynthesis of a reversely N-prenylated monomeric L-tryptophan (r-N-DMAT) (PubMed:28295904). The main product of the cluster is the r-N-DMAT produced by the dimethylallyltryptophan synthase DMATS1 and it remains unclear whether this metabolite undergoes further modifications when silent gene clusters are activated (PubMed:28295904). The acetylated form of r-N-DMAT, ac-r-N-DMAT, is also produced (PubMed:28295904). The roles of the cytochrome P450 monooxygenase FFUJ_09176 and the methyltransferase FFUJ_09178 have still to be elucidated (Probable).<ref>PMID:28295904</ref> <ref>PMID:28295904</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The regiospecific prenylation of an aromatic amino acid catalyzed by a dimethylallyl-l-tryptophan synthase (DMATS) is a key step in the biosynthesis of many fungal and bacterial natural products. DMATS enzymes share a common "ABBA" fold with divergent active site contours that direct alternative C-C, C-N, and C-O bond-forming trajectories. DMATS1 from Fusarium fujikuroi catalyzes the reverse N-prenylation of l-Trp by generating an allylic carbocation from dimethylallyl diphosphate (DMAPP) that then alkylates the indole nitrogen of l-Trp. DMATS1 stands out among the greater DMATS family because it exhibits unusually broad substrate specificity: it can utilize geranyl diphosphate (GPP) or l-Tyr as an alternative prenyl donor or acceptor, respectively; it can catalyze both forward and reverse prenylation, i.e., at C1 or C3 of DMAPP; and it can catalyze C-N and C-O bond-forming reactions. Here, we report the crystal structures of DMATS1 and its complexes with l-Trp or l-Tyr and unreactive thiolodiphosphate analogues of the prenyl donors DMAPP and GPP. Structures of ternary complexes mimic Michaelis complexes with actual substrates and illuminate active site features that govern prenylation regiochemistry. Comparison with CymD, a bacterial enzyme that catalyzes the reverse N-prenylation of l-Trp with DMAPP, indicates that bacterial and fungal DMATS enzymes share a conserved reaction mechanism. However, the narrower active site contour of CymD enforces narrower substrate specificity. Structure-function relationships established for DMATS enzymes will ultimately inform protein engineering experiments that will broaden the utility of these enzymes as useful tools for synthetic biology.

-	~~Authors~~:	+	Structural Basis of Substrate Promiscuity and Catalysis by the Reverse Prenyltransferase N-Dimethylallyl-l-tryptophan Synthase from Fusarium fujikuroi.,Eaton SA, Ronnebaum TA, Roose BW, Christianson DW Biochemistry. 2022 Sep 20;61(18):2025-2035. doi: 10.1021/acs.biochem.2c00350., Epub 2022 Sep 9. PMID:36084241<ref>PMID:36084241</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8db1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fusarium fujikuroi]]
		+	[[Category: Large Structures]]
		+	[[Category: Christianson DW]]
		+	[[Category: Eaton SA]]
		+	[[Category: Ronnebaum TA]]
		+	[[Category: Roose BW]]

OCA at 04:23, 20 July 2022

2022-07-20T04:23:56Z

←Older revision		Revision as of 04:23, 20 July 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8db1 is ON HOLD	+	The entry 8db1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8db1" [edit=sysop:move=sysop]

2022-06-22T07:28:55Z

Protected "8db1" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:28, 22 June 2022

OCA: New page: '''Unreleased structure''' The entry 8db1 is ON HOLD Authors: Description: Category: Unreleased Structures

2022-06-22T07:28:54Z

New page: '''Unreleased structure''' The entry 8db1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8db1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]