7dca - Revision history

OCA at 16:30, 29 November 2023

2023-11-29T16:30:39Z

← Older revision		Revision as of 16:30, 29 November 2023
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	<StructureSection load='7dca' size='340' side='right'caption='[[7dca]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='7dca' size='340' side='right'caption='[[7dca]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dca]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dca]] 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=7DCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCA FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=4UO:2,3~~-~~DIHYDROXANTHOSINE'>4UO</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]] 2.1Å</td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Guanosine_deaminase Guanosine deaminase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.15 3.5.4.15]~~ </~~span~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4UO:2,3-DIHYDROXANTHOSINE'>4UO</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=7dca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dca OCA], [https://pdbe.org/7dca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dca RCSB], [https://www.ebi.ac.uk/pdbsum/7dca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dca 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=7dca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dca OCA], [https://pdbe.org/7dca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dca RCSB], [https://www.ebi.ac.uk/pdbsum/7dca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dca ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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>		[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7dca" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7dca" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Deaminase 3D structures\|Deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Guanosine deaminase~~]]		[[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]]
	~~[[Category: Deamination]]~~
	~~[[Category: Gsda]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Purine metabolism~~]]

OCA at 10:50, 16 February 2022

2022-02-16T10:50:26Z

← Older revision		Revision as of 10:50, 16 February 2022
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	==The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine==		==The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine==
	<StructureSection load='7dca' size='340' side='right'caption='[[7dca]]' scene=''>		<StructureSection load='7dca' size='340' side='right'caption='[[7dca]], [[Resolution\|resolution]] 2.10Å' 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=7DCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dca]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCA 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=7dca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dca OCA], [https://pdbe.org/7dca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dca RCSB], [https://www.ebi.ac.uk/pdbsum/7dca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dca 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=4UO:2,3-DIHYDROXANTHOSINE'>4UO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Guanosine_deaminase Guanosine deaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.15 3.5.4.15] </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=7dca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dca OCA], [https://pdbe.org/7dca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dca RCSB], [https://www.ebi.ac.uk/pdbsum/7dca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dca 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 ==
			Guanosine deaminase (GSDA) in plants specifically deaminates (de)guanosine to produce xanthosine with high specificity, which is further converted to xanthine, a key intermediate in purine metabolism and nitrogen recycling. We solved GSDA's structures from Arabidopsis thaliana in the free and ligand-bound forms at high resolutions. Unlike GDA, the enzyme employs a single-proton shuttle mechanism for catalysis and both the substrate and enzyme undergo structural rearrangements. The last fragment of the enzyme loops back and seals the active site, and the substrate rotates during the reaction, both essential to deamination. We further identified more substrates that could be employed by the enzyme and compare it with other deaminases to reveal the recognition differences of specific substrates. Our studies provide insight into this important enzyme involved in purine metabolism and will potentially aid in the development of deaminase-based gene-editing tools.

			The C-terminal loop of Arabidopsis thaliana guanosine deaminase is essential to catalysis.,Jia Q, Zeng H, Li H, Xiao N, Tang J, Gao S, Zhang J, Xie W Chem Commun (Camb). 2021 Sep 23;57(76):9748-9751. doi: 10.1039/d1cc03042f. PMID:34477187<ref>PMID:34477187</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7dca" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Guanosine deaminase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Jia Q]]		[[Category: Jia, Q]]
	[[Category: Xie W]]		[[Category: Xie, W]]
	[[Category: Zeng H]]		[[Category: Zeng, H]]
			[[Category: Deamination]]
			[[Category: Gsda]]
			[[Category: Hydrolase]]
			[[Category: Purine metabolism]]

OCA at 08:48, 29 September 2021

2021-09-29T08:48:01Z

← Older revision		Revision as of 08:48, 29 September 2021
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	~~'''Unreleased structure'''~~

	The ~~entry~~ 7dca is ~~ON HOLD until Oct 23 2022~~		==The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine==
			<StructureSection load='7dca' size='340' side='right'caption='[[7dca]]' 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=7DCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DCA FirstGlance]. <br>
	~~Description: The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine~~		</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=7dca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dca OCA], [https://pdbe.org/7dca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dca RCSB], [https://www.ebi.ac.uk/pdbsum/7dca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dca ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Zeng, H~~]]		__TOC__
	[[Category: Xie, W]]		</StructureSection>
	[[Category: ~~Jia, Q~~]]		[[Category: Large Structures]]
			[[Category: Jia Q]]
			[[Category: Xie W]]
			[[Category: Zeng H]]

OCA at 05:29, 4 November 2020

2020-11-04T05:29:20Z

← Older revision		Revision as of 05:29, 4 November 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7dca is ON HOLD		The entry 7dca is ON HOLD until Oct 23 2022

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

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

2020-10-28T19:05:30Z

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

← Older revision	Revision as of 19:05, 28 October 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7dca is ON HOLD Authors: Xie, W., Jia, Q., Zeng, H. Description: The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine ...

2020-10-28T19:05:29Z

New page: '''Unreleased structure''' The entry 7dca is ON HOLD Authors: Xie, W., Jia, Q., Zeng, H. Description: The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine ...

New page

'''Unreleased structure'''

The entry 7dca is ON HOLD

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

Description: The structure of the Arabidopsis thaliana guanosine deaminase bound by xanthosine
[[Category: Unreleased Structures]]
[[Category: Zeng, H]]
[[Category: Xie, W]]
[[Category: Jia, Q]]