7dbf - Revision history

OCA at 16:30, 29 November 2023

2023-11-29T16:30:14Z

← Older revision		Revision as of 16:30, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7dbf' size='340' side='right'caption='[[7dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='7dbf' size='340' side='right'caption='[[7dbf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dbf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dbf]] 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=7DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBF FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.9Å</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=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=7dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbf OCA], [https://pdbe.org/7dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbf RCSB], [https://www.ebi.ac.uk/pdbsum/7dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbf 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=7dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbf OCA], [https://pdbe.org/7dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbf RCSB], [https://www.ebi.ac.uk/pdbsum/7dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbf 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 ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7dbf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7dbf" 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

2022-02-16T10:50:08Z

← Older revision		Revision as of 10:50, 16 February 2022
Line 1:		Line 1:

	==The structure of the Arabidopsis thaliana guanosine deaminase==		==The structure of the Arabidopsis thaliana guanosine deaminase==
	<StructureSection load='7dbf' size='340' side='right'caption='[[7dbf]]' scene=''>		<StructureSection load='7dbf' size='340' side='right'caption='[[7dbf]], [[Resolution\|resolution]] 1.90Å' 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=7DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dbf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBF 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=7dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbf OCA], [https://pdbe.org/7dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbf RCSB], [https://www.ebi.ac.uk/pdbsum/7dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbf 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=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=7dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbf OCA], [https://pdbe.org/7dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbf RCSB], [https://www.ebi.ac.uk/pdbsum/7dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbf 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 7dbf" 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 08:47, 29 September 2021

2021-09-29T08:47:56Z

← Older revision		Revision as of 08:47, 29 September 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	The ~~entry~~ 7dbf is ~~ON HOLD until Oct 20 2022~~		==The structure of the Arabidopsis thaliana guanosine deaminase==
			<StructureSection load='7dbf' size='340' side='right'caption='[[7dbf]]' 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=7DBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBF FirstGlance]. <br>
	~~Description: The structure of the Arabidopsis thaliana guanosine deaminase~~		</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=7dbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbf OCA], [https://pdbe.org/7dbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbf RCSB], [https://www.ebi.ac.uk/pdbsum/7dbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbf 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 05:28, 4 November 2020

2020-11-04T05:28:44Z

← Older revision		Revision as of 05:28, 4 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7dbf is ON HOLD		The entry 7dbf is ON HOLD until Oct 20 2022

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

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

2020-10-28T19:03:48Z

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

← Older revision	Revision as of 19:03, 28 October 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7dbf is ON HOLD Authors: Xie, W., Jia, Q., Zeng, H. Description: The structure of the Arabidopsis thaliana guanosine deaminase [[Category: Unreleas...

2020-10-28T19:03:46Z

New page: '''Unreleased structure''' The entry 7dbf is ON HOLD Authors: Xie, W., Jia, Q., Zeng, H. Description: The structure of the Arabidopsis thaliana guanosine deaminase [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 7dbf is ON HOLD

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

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