6k5m - Revision history

OCA at 06:55, 22 September 2021

2021-09-22T06:55:18Z

←Older revision		Revision as of 06:55, 22 September 2021
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Plant tryptophan decarboxylase~~ (~~TDC~~) is ~~a type II Pyridoxal~~-5'-~~phosphate~~-~~dependent decarboxylase (PLP_DC~~) ~~that could be used as a target to genetically improve crops. However~~, ~~lack of accurate structural information on plant TDC hampers the understanding~~ of its ~~decarboxylation~~ mechanisms. ~~In the present study~~, ~~the crystal structures~~ of Oryza sativa ~~TDC~~ (~~OsTDC~~) ~~in its complexes with pyridoxal-5'-phosphate, tryptamine and serotonin were determined~~. ~~The~~ structures ~~provide detailed interaction information between TDC and its substrates. The Y359 residue from~~ the ~~loop gate is a proton donor~~ and forms ~~a Lewis acid~~-~~base pair with~~ serotonin~~/tryptamine~~, ~~which is associated with product release. The H214 residue is responsible for PLP binding~~ and ~~proton transfer, and its proper interaction with Y359 is essential for OsTDC enzyme activity. The extra hydrogen bonds formed between the~~ 5-~~hydroxyl group of serotonin and~~ the ~~backbone carboxyl groups~~ of ~~F104 and P105 explain the discrepancy between the catalytic activity of TDC in tryptophan and in 5~~-~~hydroxytryptophan~~. ~~In addition~~, ~~an evolutionary analysis revealed that type II PLP_DC originated from glutamic acid decarboxylase~~, ~~potentially as an adaptive evolution of mechanism in organisms in extreme environments. This study is~~, ~~to our knowledge~~, the ~~first to present a detailed analysis of the crystal structure of OsTDC~~ in ~~these complexes~~. ~~The information regarding the~~ catalytic mechanism ~~described here could facilitate the development of protocols to regulate melatonin levels~~ and ~~thereby contribute to crop improvement efforts to improve food security worldwide~~.	+	Serotonin N-acetyltransferase (SNAT) is the key rate-limiting enzyme in melatonin biosynthesis. It mediates melatonin biosynthesis in plants by using serotonin and 5-methoxytryptamine (5-MT), but little is known of its underlying mechanisms. Herein, we present a detailed reaction mechanism of a SNAT from Oryza sativa through combined structural and molecular dynamics (MD) analysis. We report the crystal structures of plant SNAT in the apo and binary/ternary complex forms with acetyl-CoA (AcCoA), serotonin, and 5-MT. OsSNAT exhibits a unique enzymatically active dimeric fold not found in the known structures of arylalkylamine N-acetyltransferase (AANAT) family. The key residues W188, D189, D226, N220, and Y233 located around the active pocket are important in catalysis, confirmed by site-directed mutagenesis. Combined with MD simulations, we hypothesize a novel plausible catalytic mechanism in which D226 and Y233 function as catalytic base and acid during the acetyl-transfer reaction.

-	~~Crystal structure~~ of ~~Oryza sativa TDC reveals the substrate specificity for TDC~~-~~mediated melatonin biosynthesis~~.,Zhou Y, ~~Liao L~~, Liu X, Liu B, Chen X, Guo Y, ~~Huang C~~, Zhao Y~~, Zeng Z J Adv Res~~. ~~2020 Jun 12~~;24:~~501~~-~~511~~. doi: 10.~~1016~~/j.~~jare~~.~~2020.06.004. eCollection, 2020 Jul~~. PMID:~~32595985~~<ref>PMID:~~32595985~~</ref>	+	Structural and Molecular Dynamics Analysis of Plant Serotonin N-Acetyltransferase Reveal an Acid/Base-Assisted Catalysis in Melatonin Biosynthesis.,Liao L, Zhou Y, Xu Y, Zhang Y, Liu X, Liu B, Chen X, Guo Y, Zeng Z, Zhao Y Angew Chem Int Ed Engl. 2021 May 17;60(21):12020-12026. doi:, 10.1002/anie.202100992. Epub 2021 Apr 7. PMID:33682300<ref>PMID:33682300</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 15:15, 8 June 2021

2021-06-08T15:15:30Z

←Older revision		Revision as of 15:15, 8 June 2021
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	<StructureSection load='6k5m' size='340' side='right'caption='[[6k5m]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='6k5m' size='340' side='right'caption='[[6k5m]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k5m]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6K5M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k5m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K5M FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNAT1, GNAT5, NSI, SNAT, Os05g0481000, LOC_Os05g40260, OsJ_018182, OsJ_18949, OSJNBa0095J22.4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNAT1, GNAT5, NSI, SNAT, Os05g0481000, LOC_Os05g40260, OsJ_018182, OsJ_18949, OSJNBa0095J22.4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=6k5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5m OCA], [~~http~~://pdbe.org/6k5m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k5m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k5m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5m 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=6k5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5m OCA], [https://pdbe.org/6k5m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k5m RCSB], [https://www.ebi.ac.uk/pdbsum/6k5m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SNAT1_ORYSJ SNAT1_ORYSJ]] Catalyzes the N-acetylation of serotonin into N-acetylserotonin, the penultimate step in the synthesis of melatonin (PubMed:22998587, PubMed:24134674, PubMed:27121038). Catalyzes in vitro the N-acetylation of tryptamine to produce N-acetyltryptamine, 5-methoxytryptamine to produce melatonin and tyramine to produce N-acetyltyramine (PubMed:27121038). Acetyltransferase required for geminivirus infection and systemic spread (By similarity).[UniProtKB:Q7X9V3]<ref>PMID:22998587</ref> <ref>PMID:24134674</ref> <ref>PMID:27121038</ref>	+	[[https://www.uniprot.org/uniprot/SNAT1_ORYSJ SNAT1_ORYSJ]] Catalyzes the N-acetylation of serotonin into N-acetylserotonin, the penultimate step in the synthesis of melatonin (PubMed:22998587, PubMed:24134674, PubMed:27121038). Catalyzes in vitro the N-acetylation of tryptamine to produce N-acetyltryptamine, 5-methoxytryptamine to produce melatonin and tyramine to produce N-acetyltyramine (PubMed:27121038). Acetyltransferase required for geminivirus infection and systemic spread (By similarity).[UniProtKB:Q7X9V3]<ref>PMID:22998587</ref> <ref>PMID:24134674</ref> <ref>PMID:27121038</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6k5m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k5m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serotonin N-acetyltransferase\|Serotonin N-acetyltransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:51, 20 July 2020

2020-07-20T08:51:29Z

←Older revision		Revision as of 08:51, 20 July 2020
Line 1:		Line 1:

-	==n/a==	+	==The crystal structure of a serotonin N-acetyltransferase from Oryza Sativa (Rice)==
-	<StructureSection load='6k5m' size='340' side='right'caption='[[6k5m]]' scene=''>	+	<StructureSection load='6k5m' size='340' side='right'caption='[[6k5m]], [[Resolution\|resolution]] 1.79Å' 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=6K5M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K5M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k5m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K5M 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=6k5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5m OCA], [http://pdbe.org/6k5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5m RCSB], [http://www.ebi.ac.uk/pdbsum/6k5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5m ProSAT]</span></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNAT1, GNAT5, NSI, SNAT, Os05g0481000, LOC_Os05g40260, OsJ_018182, OsJ_18949, OSJNBa0095J22.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=6k5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5m OCA], [http://pdbe.org/6k5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5m RCSB], [http://www.ebi.ac.uk/pdbsum/6k5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SNAT1_ORYSJ SNAT1_ORYSJ]] Catalyzes the N-acetylation of serotonin into N-acetylserotonin, the penultimate step in the synthesis of melatonin (PubMed:22998587, PubMed:24134674, PubMed:27121038). Catalyzes in vitro the N-acetylation of tryptamine to produce N-acetyltryptamine, 5-methoxytryptamine to produce melatonin and tyramine to produce N-acetyltyramine (PubMed:27121038). Acetyltransferase required for geminivirus infection and systemic spread (By similarity).[UniProtKB:Q7X9V3]<ref>PMID:22998587</ref> <ref>PMID:24134674</ref> <ref>PMID:27121038</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant tryptophan decarboxylase (TDC) is a type II Pyridoxal-5'-phosphate-dependent decarboxylase (PLP_DC) that could be used as a target to genetically improve crops. However, lack of accurate structural information on plant TDC hampers the understanding of its decarboxylation mechanisms. In the present study, the crystal structures of Oryza sativa TDC (OsTDC) in its complexes with pyridoxal-5'-phosphate, tryptamine and serotonin were determined. The structures provide detailed interaction information between TDC and its substrates. The Y359 residue from the loop gate is a proton donor and forms a Lewis acid-base pair with serotonin/tryptamine, which is associated with product release. The H214 residue is responsible for PLP binding and proton transfer, and its proper interaction with Y359 is essential for OsTDC enzyme activity. The extra hydrogen bonds formed between the 5-hydroxyl group of serotonin and the backbone carboxyl groups of F104 and P105 explain the discrepancy between the catalytic activity of TDC in tryptophan and in 5-hydroxytryptophan. In addition, an evolutionary analysis revealed that type II PLP_DC originated from glutamic acid decarboxylase, potentially as an adaptive evolution of mechanism in organisms in extreme environments. This study is, to our knowledge, the first to present a detailed analysis of the crystal structure of OsTDC in these complexes. The information regarding the catalytic mechanism described here could facilitate the development of protocols to regulate melatonin levels and thereby contribute to crop improvement efforts to improve food security worldwide.
		+
		+	Crystal structure of Oryza sativa TDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis.,Zhou Y, Liao L, Liu X, Liu B, Chen X, Guo Y, Huang C, Zhao Y, Zeng Z J Adv Res. 2020 Jun 12;24:501-511. doi: 10.1016/j.jare.2020.06.004. eCollection, 2020 Jul. PMID:32595985<ref>PMID:32595985</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k5m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Japanese rice]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~N/a~~]]	+	[[Category: Guo, Y]]
		+	[[Category: Liao, L J]]
		+	[[Category: Liu, X K]]
		+	[[Category: Zeng, Z X]]
		+	[[Category: Zhao, Y C]]
		+	[[Category: Zhou, Y Z]]
		+	[[Category: Serotonin n-acetyltransferase]]
		+	[[Category: Transferase]]

OCA at 06:26, 3 June 2020

2020-06-03T06:26:28Z

←Older revision		Revision as of 06:26, 3 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k5m ~~is ON HOLD until Paper Publication~~	+	==n/a==
-		+	<StructureSection load='6k5m' size='340' side='right'caption='[[6k5m]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K5M 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=6k5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5m OCA], [http://pdbe.org/6k5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5m RCSB], [http://www.ebi.ac.uk/pdbsum/6k5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5m ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: N/a]]

OCA at 03:52, 12 June 2019

2019-06-12T03:52:00Z

←Older revision		Revision as of 03:52, 12 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k5m is ON HOLD	+	The entry 6k5m is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6k5m" [edit=sysop:move=sysop]

2019-06-05T21:02:11Z

Protected "6k5m" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:02, 5 June 2019

OCA: New page: '''Unreleased structure''' The entry 6k5m is ON HOLD Authors: Description: Category: Unreleased Structures

2019-06-05T21:02:09Z

New page: '''Unreleased structure''' The entry 6k5m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6k5m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]