OCA at 07:10, 9 October 2024

2024-10-09T07:10:26Z

← Older revision		Revision as of 07:10, 9 October 2024
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	~~'''Unreleased structure'''~~

	~~The entry~~ 9jer is ~~ON HOLD until Paper~~ Publication		==Arginine decarboxylase in Aspergillus oryzae, ligand-free form==
			<StructureSection load='9jer' size='340' side='right'caption='[[9jer]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[9jer]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9JER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9JER FirstGlance]. <br>
			</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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=9jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9jer OCA], [https://pdbe.org/9jer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9jer RCSB], [https://www.ebi.ac.uk/pdbsum/9jer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9jer ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q2UAM5_ASPOR Q2UAM5_ASPOR]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Agmatine, a natural polyamine also known as 4-aminobutyl-guanidine, is biosynthesized from arginine by decarboxylation. Aspergillus oryzae contains high amounts of agmatine, suggesting highly active arginine decarboxylase (ADC) in this organism. However, genome analysis revealed no ADC homolog in A. oryzae. A. oryzae strain RIB40 has six homologs of phosphatidylserine decarboxylase (PSD), an enzyme that synthesizes phosphatidyl ethanolamine from phosphatidylserine. We previously discovered that one of these homologs, AO090102000327, encodes arginine decarboxylase, which we named ADC1. In the present study, we determined the crystal structures of ligand-free, arginine-treated, and agmatine-treated ADC1 each at 1.9-2.15 A resolution. Each structure contained four ADC1 molecules (chains A-D) in the asymmetric unit of the cell. Each ADC1 molecule is a heterodimer consisting of the N-terminal region (Asn60-Gly441) and C-terminal region (Ser442-Thr482). In the ligand-free ADC1, the N-terminus of Ser442 was modified to form a pyruvoyl group. In the arginine-treated ADC1, arginine was converted to agmatine, with the pyruvoyl group covalently bound to agmatine by forming a Schiff base. The same structure was observed in agmatine-treated ADC1. These results indicate that ADC1 is a pyruvoyl-dependent decarboxylase and unveils the reaction mechanism of ADC from A. oryzae.

	~~Authors~~: ~~Mikami, B~~., ~~Yaukawa~~, ~~K., Fujiwara, S.~~, Takita, T., Mizutani, K., ~~Odagaki, Y~~.~~, Murakami, Y~~.		Unveiling the reaction mechanism of arginine decarboxylase in Aspergillus oryzae: Insights from crystal structure analysis.,Odagaki Y, Murakami Y, Takita T, Mizutani K, Mikami B, Fujiwara S, Yasukawa K Biochem Biophys Res Commun. 2024 Nov 12;733:150728. doi: , 10.1016/j.bbrc.2024.150728. Epub 2024 Sep 21. PMID:39321488<ref>PMID:39321488</ref>

	~~Description: Arginine decarboxylase in Aspergillus oryzae~~, ~~ligand~~-~~free form~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
	[[Category: ~~Mizutani, K~~]]		<div class="pdbe-citations 9jer" style="background-color:#fffaf0;"></div>
	[[Category: ~~Murakami, Y~~]]		== References ==
	[[Category: ~~Fujiwara, S~~]]		<references/>
	[[Category: ~~Yaukawa,~~ K]]		__TOC__
	[[Category: ~~Takita, T~~]]		</StructureSection>
	[[Category: Odagaki, Y]]		[[Category: Aspergillus oryzae RIB40]]
	[[Category: ~~Mikami, B~~]]		[[Category: Large Structures]]
			[[Category: Fujiwara S]]
			[[Category: Mikami B]]
			[[Category: Mizutani K]]
			[[Category: Murakami Y]]
			[[Category: Odagaki Y]]
			[[Category: Takita T]]
			[[Category: Yasukawa K]]

OCA at 04:01, 18 September 2024

2024-09-18T04:01:49Z

← Older revision		Revision as of 04:01, 18 September 2024
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 9jer is ON HOLD		The entry 9jer is ON HOLD until Paper Publication

	Authors: Mikami, B., Yaukawa, K., Fujiwara, S., Takita, T., Mizutani, K., Odagaki, Y., Murakami, Y.		Authors: Mikami, B., Yaukawa, K., Fujiwara, S., Takita, T., Mizutani, K., Odagaki, Y., Murakami, Y.
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	Description: Arginine decarboxylase in Aspergillus oryzae, ligand-free form		Description: Arginine decarboxylase in Aspergillus oryzae, ligand-free form
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Mizutani, K]]
			[[Category: Murakami, Y]]
	[[Category: Fujiwara, S]]		[[Category: Fujiwara, S]]
	[[Category: ~~Murakami~~, ~~Y]]~~		[[Category: Yaukawa, K]]
	~~[[Category: Mikami, B~~]]
	[[Category: Takita, T]]		[[Category: Takita, T]]
	[[Category: Odagaki, Y]]		[[Category: Odagaki, Y]]
	[[Category: ~~Yaukawa~~, ~~K]]~~		[[Category: Mikami, B]]
	~~[[Category: Mizutani, K~~]]

OCA: Protected "9jer" [edit=sysop:move=sysop]

2024-09-11T05:17:32Z

Protected "9jer" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:17, 11 September 2024
(No difference)

OCA: New page: '''Unreleased structure''' The entry 9jer is ON HOLD Authors: Mikami, B., Yaukawa, K., Fujiwara, S., Takita, T., Mizutani, K., Odagaki, Y., Murakami, Y. Description: Arginine decarboxy...

2024-09-11T05:17:31Z

New page: '''Unreleased structure''' The entry 9jer is ON HOLD Authors: Mikami, B., Yaukawa, K., Fujiwara, S., Takita, T., Mizutani, K., Odagaki, Y., Murakami, Y. Description: Arginine decarboxy...

New page

'''Unreleased structure'''

The entry 9jer is ON HOLD

Authors: Mikami, B., Yaukawa, K., Fujiwara, S., Takita, T., Mizutani, K., Odagaki, Y., Murakami, Y.

Description: Arginine decarboxylase in Aspergillus oryzae, ligand-free form
[[Category: Unreleased Structures]]
[[Category: Fujiwara, S]]
[[Category: Murakami, Y]]
[[Category: Mikami, B]]
[[Category: Takita, T]]
[[Category: Odagaki, Y]]
[[Category: Yaukawa, K]]
[[Category: Mizutani, K]]

9jer - Revision history

OCA at 07:10, 9 October 2024

OCA at 04:01, 18 September 2024

OCA: Protected "9jer" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 9jer is ON HOLD Authors: Mikami, B., Yaukawa, K., Fujiwara, S., Takita, T., Mizutani, K., Odagaki, Y., Murakami, Y. Description: Arginine decarboxy...