1wkq - Revision history

OCA at 13:31, 13 March 2024

OCA — Wed, 13 Mar 2024 13:31:50 GMT

←Older revision		Revision as of 13:31, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wkq' size='340' side='right'caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='1wkq' size='340' side='right'caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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]] 1.17Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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~~'>~~[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3]~~ </~~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=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [https://pdbe.org/1wkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [https://www.ebi.ac.uk/pdbsum/1wkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkq ProSAT]</span></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=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [~~http~~://pdbe.org/1wkq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wkq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkq ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GUAD_BACSU GUAD_BACSU]] Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia.	+	[https://www.uniprot.org/uniprot/GUAD_BACSU GUAD_BACSU] Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wkq ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wkq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexpectedly, the C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface of 3900 A(2) per monomer. The essential zinc ion is ligated by a water molecule together with His(53), Cys(83), and Cys(86). A transition state analog was modeled into the active site cavity based on the tightly bound imidazole and water molecules, allowing identification of the conserved deamination mechanism and specific substrate recognition by Asp(114) and Tyr(156'). The closed conformation also reveals that substrate binding seals the active site entrance, which is controlled by the C-terminal tail. Therefore, the domain swapping has not only facilitated the dimerization but has also ensured specific substrate recognition. Finally, a detailed structural comparison of the cytidine deaminase superfamily illustrates the functional versatility of the divergent active sites found in the guanine, cytosine, and cytidine deaminases and suggests putative specific substrate-interacting residues for other members such as dCMP deaminases.
-
-	Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily.,Liaw SH, Chang YJ, Lai CT, Chang HC, Chang GG J Biol Chem. 2004 Aug 20;279(34):35479-85. Epub 2004 Jun 4. PMID:15180998<ref>PMID:15180998</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wkq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Deaminase 3D structures\|Deaminase 3D structures]]		*[[Deaminase 3D structures\|Deaminase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835]]~~	+	[[Category: Bacillus subtilis]]
-	~~[[Category: Guanine deaminase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang~~, Y J~~]]	+	[[Category: Chang YJ]]
-	[[Category: Lai~~, C T~~]]	+	[[Category: Lai CT]]
-	[[Category: Liaw~~, S H]]~~	+	[[Category: Liaw SH]]
-	~~[[Category: Domain swap]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Structural plasticity]]~~	+
-	~~[[Category: Substrate specificity]]~~	+
-	~~[[Category: The cytidine deaminase superfamily~~]]	+

OCA at 09:23, 6 January 2021

OCA — Wed, 06 Jan 2021 09:23:39 GMT

←Older revision		Revision as of 09:23, 6 January 2021
Line 1:		Line 1:

	==Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily==		==Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily==
-	<StructureSection load='1wkq' size='340' side='right' caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>	+	<StructureSection load='1wkq' size='340' side='right'caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://pdbe.org/1wkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkq ProSAT]</span></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=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://pdbe.org/1wkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Deaminase\|Deaminase]]	+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Guanine deaminase]]		[[Category: Guanine deaminase]]
		+	[[Category: Large Structures]]
	[[Category: Chang, Y J]]		[[Category: Chang, Y J]]
	[[Category: Lai, C T]]		[[Category: Lai, C T]]

OCA at 16:24, 11 April 2018

OCA — Wed, 11 Apr 2018 16:24:07 GMT

←Older revision		Revision as of 16:24, 11 April 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily==		==Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily==
	<StructureSection load='1wkq' size='340' side='right' caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='1wkq' size='340' side='right' caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://pdbe.org/1wkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://pdbe.org/1wkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wk/1wkq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wk/1wkq_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Guanine deaminase]]		[[Category: Guanine deaminase]]
	[[Category: Chang, Y J]]		[[Category: Chang, Y J]]

OCA at 13:19, 7 February 2016

OCA — Sun, 07 Feb 2016 13:19:35 GMT

←Older revision		Revision as of 13:19, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wkq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:50, 10 September 2015

OCA — Thu, 10 Sep 2015 01:50:07 GMT

←Older revision		Revision as of 01:50, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1wkq' size='340' side='right' caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='1wkq' size='340' side='right' caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://pdbe.org/1wkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 1wkq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Guanine deaminase]]		[[Category: Guanine deaminase]]
	[[Category: Chang, Y J]]		[[Category: Chang, Y J]]

OCA at 15:22, 24 December 2014

OCA — Wed, 24 Dec 2014 15:22:14 GMT

←Older revision		Revision as of 15:22, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GUAD_BACSU GUAD_BACSU]] Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Guanine deaminase]]		[[Category: Guanine deaminase]]
-	[[Category: Chang, Y J.]]	+	[[Category: Chang, Y J]]
-	[[Category: Lai, C T.]]	+	[[Category: Lai, C T]]
-	[[Category: Liaw, S H.]]	+	[[Category: Liaw, S H]]
	[[Category: Domain swap]]		[[Category: Domain swap]]
-	[[Category: Guanine deaminase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Structural plasticity]]		[[Category: Structural plasticity]]
	[[Category: Substrate specificity]]		[[Category: Substrate specificity]]
	[[Category: The cytidine deaminase superfamily]]		[[Category: The cytidine deaminase superfamily]]

OCA at 21:01, 29 September 2014

OCA — Mon, 29 Sep 2014 21:01:06 GMT

←Older revision		Revision as of 21:01, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wkq.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily==
		+	<StructureSection load='1wkq' size='340' side='right' caption='[[1wkq]], [[Resolution\|resolution]] 1.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">guanine deaminase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [http://www.ebi.ac.uk/pdbsum/1wkq PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wk/1wkq_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexpectedly, the C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface of 3900 A(2) per monomer. The essential zinc ion is ligated by a water molecule together with His(53), Cys(83), and Cys(86). A transition state analog was modeled into the active site cavity based on the tightly bound imidazole and water molecules, allowing identification of the conserved deamination mechanism and specific substrate recognition by Asp(114) and Tyr(156'). The closed conformation also reveals that substrate binding seals the active site entrance, which is controlled by the C-terminal tail. Therefore, the domain swapping has not only facilitated the dimerization but has also ensured specific substrate recognition. Finally, a detailed structural comparison of the cytidine deaminase superfamily illustrates the functional versatility of the divergent active sites found in the guanine, cytosine, and cytidine deaminases and suggests putative specific substrate-interacting residues for other members such as dCMP deaminases.

-	~~{{STRUCTURE_1wkq\| PDB=1wkq \| SCENE= }}~~	+	Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily.,Liaw SH, Chang YJ, Lai CT, Chang HC, Chang GG J Biol Chem. 2004 Aug 20;279(34):35479-85. Epub 2004 Jun 4. PMID:15180998<ref>PMID:15180998</ref>

-	~~===Crystal Structure~~ of ~~Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in~~ the ~~cytidine deaminase superfamily===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15180998}}~~	+	==See Also==
-		+	*[[Deaminase\|Deaminase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1wkq~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015180998<~~/~~ref~~><~~ref group="xtra">PMID:015159585</ref><references group="xtra"~~/>	+
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Guanine deaminase]]		[[Category: Guanine deaminase]]

OCA at 12:14, 23 January 2013

OCA — Wed, 23 Jan 2013 12:14:05 GMT

←Older revision		Revision as of 12:14, 23 January 2013
Line 1:		Line 1:
	[[Image:1wkq.png\|left\|200px]]		[[Image:1wkq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wkq", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1wkq\| PDB=1wkq \| SCENE= }}		{{STRUCTURE_1wkq\| PDB=1wkq \| SCENE= }}

	===Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily===		===Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15180998}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15180998 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15180998}}		{{ABSTRACT_PUBMED_15180998}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15180998~~</ref><ref group="xtra">PMID:~~15159585~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015180998</ref><ref group="xtra">PMID:015159585</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Guanine deaminase]]		[[Category: Guanine deaminase]]

OCA: Protected "1wkq" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 20:30:39 GMT

Protected "1wkq" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:30, 14 March 2011

OCA at 20:30, 14 March 2011

OCA — Mon, 14 Mar 2011 20:30:37 GMT

←Older revision		Revision as of 20:30, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wkq.png\|left\|200px]]		[[Image:1wkq.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~1WKQ~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA].	+	[[1wkq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA].

	==Reference==		==Reference==
Line 35:		Line 34:
	[[Category: Substrate specificity]]		[[Category: Substrate specificity]]
	[[Category: The cytidine deaminase superfamily]]		[[Category: The cytidine deaminase superfamily]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 16 08:27:17 2009''