7dqn - Revision history

OCA at 16:38, 29 November 2023

OCA — Wed, 29 Nov 2023 16:38:12 GMT

←Older revision		Revision as of 16:38, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dqn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DQN FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dqn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DQN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMP:GUANOSINE'>GMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMP:GUANOSINE'>GMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7dqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dqn OCA], [https://pdbe.org/7dqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dqn RCSB], [https://www.ebi.ac.uk/pdbsum/7dqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dqn 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=7dqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dqn OCA], [https://pdbe.org/7dqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dqn RCSB], [https://www.ebi.ac.uk/pdbsum/7dqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dqn ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:32, 15 February 2023

OCA — Wed, 15 Feb 2023 10:32:25 GMT

←Older revision		Revision as of 10:32, 15 February 2023
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	==The structure of the Arabidopsis thaliana guanosine deaminase mutant Y185F complexed with guanosine==		==The structure of the Arabidopsis thaliana guanosine deaminase mutant Y185F complexed with guanosine==
-	<StructureSection load='7dqn' size='340' side='right'caption='[[7dqn]]' scene=''>	+	<StructureSection load='7dqn' size='340' side='right'caption='[[7dqn]], [[Resolution\|resolution]] 2.60Å' 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=7DQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DQN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dqn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DQN FirstGlance]. <br>
-	</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=7dqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dqn OCA], [https://pdbe.org/7dqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dqn RCSB], [https://www.ebi.ac.uk/pdbsum/7dqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dqn ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMP:GUANOSINE'>GMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7dqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dqn OCA], [https://pdbe.org/7dqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dqn RCSB], [https://www.ebi.ac.uk/pdbsum/7dqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dqn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GSDA_ARATH GSDA_ARATH] Catalyzes the hydrolytic deamination of guanosine, producing xanthosine and ammonia. Deaminates exclusively guanosine and 2'-deoxyguanosine but no other aminated purines, pyrimidines, or pterines. Deamination of guanosine by GSDA is the only source of xanthosine production in Arabidopsis.<ref>PMID:24130159</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In plants, guanosine deaminase (GSDA) catalyzes the deamination of guanosine for nitrogen recycling and re-utilization. We previously solved crystal structures of GSDA from Arabidopsis thaliana (AtGSDA) and identified several novel substrates for this enzyme, but the structural basis of the enzyme activation/inhibition is poorly understood. Here, we continued to solve 8 medium-to-high resolution (1.85-2.60 A) cocrystal structures, which involved AtGSDA and its variants bound by a few ligands, and investigated their binding modes through structural studies and thermal shift analysis. Besides the lack of a 2-amino group of these guanosine derivatives, we discovered that AtGSDA's inactivity was due to the its inability to seclude its active site. Furthermore, the C-termini of the enzyme displayed conformational diversities under certain circumstances. The lack of functional amino groups or poor interactions/geometries of the ligands at the active sites to meet the precise binding and activation requirements for deamination both contributed to AtGSDA's inactivity toward the ligands. Altogether, our combined structural and biochemical studies provide insight into GSDA.
		+
		+	Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies.,Jia Q, Zhang J, Zeng H, Tang J, Xiao N, Gao S, Li H, Xie W Int J Mol Sci. 2022 Nov 29;23(23):14976. doi: 10.3390/ijms232314976. PMID:36499303<ref>PMID:36499303</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dqn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Jia Q]]		[[Category: Jia Q]]
	[[Category: Xie W]]		[[Category: Xie W]]
	[[Category: Zeng H]]		[[Category: Zeng H]]

OCA at 06:58, 2 February 2022

OCA — Wed, 02 Feb 2022 06:58:10 GMT

←Older revision		Revision as of 06:58, 2 February 2022
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-	'''Unreleased structure'''

-	The ~~entry~~ 7dqn ~~is ON HOLD until Jan 27 2023~~	+	==The structure of the Arabidopsis thaliana guanosine deaminase mutant Y185F complexed with guanosine==
-		+	<StructureSection load='7dqn' size='340' side='right'caption='[[7dqn]]' scene=''>
-	~~Authors~~: ~~Xie~~, W., ~~Jia~~, Q., ~~Zeng~~, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DQN FirstGlance]. <br>
-	~~Description: The structure of the Arabidopsis thaliana guanosine deaminase mutant Y185F complexed with guanosine~~	+	</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=7dqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dqn OCA], [https://pdbe.org/7dqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dqn RCSB], [https://www.ebi.ac.uk/pdbsum/7dqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dqn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Xie, W~~]]	+	__TOC__
-	[[Category: ~~Zeng, H~~]]	+	</StructureSection>
-	[[Category: ~~Jia, Q~~]]	+	[[Category: Large Structures]]
		+	[[Category: Jia Q]]
		+	[[Category: Xie W]]
		+	[[Category: Zeng H]]

OCA at 11:55, 17 November 2021

OCA — Wed, 17 Nov 2021 11:55:52 GMT

←Older revision		Revision as of 11:55, 17 November 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dqn is ON HOLD until ~~Dec 24 2022~~	+	The entry 7dqn is ON HOLD until Jan 27 2023

	Authors: Xie, W., Jia, Q., Zeng, H.		Authors: Xie, W., Jia, Q., Zeng, H.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Xie, W]]		[[Category: Xie, W]]
-	[[Category: Jia, Q]]
	[[Category: Zeng, H]]		[[Category: Zeng, H]]
		+	[[Category: Jia, Q]]

OCA at 06:46, 20 January 2021

OCA — Wed, 20 Jan 2021 06:46:44 GMT

←Older revision		Revision as of 06:46, 20 January 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dqn is ON HOLD	+	The entry 7dqn is ON HOLD until Dec 24 2022

	Authors: Xie, W., Jia, Q., Zeng, H.		Authors: Xie, W., Jia, Q., Zeng, H.

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

OCA — Wed, 30 Dec 2020 05:24:12 GMT

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

←Older revision

Revision as of 05:24, 30 December 2020

OCA: New page: '''Unreleased structure''' The entry 7dqn is ON HOLD Authors: Xie, W., Jia, Q., Zeng, H. Description: The structure of the Arabidopsis thaliana guanosine deaminase mutant Y185F complex...

OCA — Wed, 30 Dec 2020 05:24:11 GMT

New page: '''Unreleased structure''' The entry 7dqn is ON HOLD Authors: Xie, W., Jia, Q., Zeng, H. Description: The structure of the Arabidopsis thaliana guanosine deaminase mutant Y185F complex...

New page

'''Unreleased structure'''

The entry 7dqn is ON HOLD

Authors: Xie, W., Jia, Q., Zeng, H.

Description: The structure of the Arabidopsis thaliana guanosine deaminase mutant Y185F complexed with guanosine
[[Category: Unreleased Structures]]
[[Category: Xie, W]]
[[Category: Jia, Q]]
[[Category: Zeng, H]]