1r9g - Revision history

OCA at 08:21, 1 May 2024

OCA — Wed, 01 May 2024 08:21:16 GMT

←Older revision		Revision as of 08:21, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='1r9g' size='340' side='right'caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1r9g' size='340' side='right'caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1R9G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R9G FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>YAAE, BSU00120 ([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=MSE:SELENOMETHIONINE'>MSE</scene></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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [~~http~~://pdbe.org/1r9g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1r9g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9g 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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [https://pdbe.org/1r9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [https://www.ebi.ac.uk/pdbsum/1r9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PDXT_BACSU PDXT_BACSU]] Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS.	+	[https://www.uniprot.org/uniprot/PDXT_BACSU PDXT_BACSU] Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		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=1r9g 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=1r9g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of YaaE from Bacillus subtilis was determined at 2.5-A resolution. YaaE is a member of the triad glutamine aminotransferase family and functions in a recently identified alternate pathway for the biosynthesis of vitamin B(6). Proposed active residues include conserved Cys-79, His-170, and Glu-172. YaaE shows similarity to HisH, a glutaminase involved in histidine biosynthesis. YaaD associates with YaaE. A homology model of this protein was constructed. YaaD is predicted to be a (beta/alpha)(8) barrel on the basis of sequence comparisons. The predicted active site includes highly conserved residues 211-216 and 233-235. Finally, a homology model of a putative YaaD-YaaE complex was prepared using the structure of HisH-F as a model. This model predicts that the ammonia molecule generated by YaaE is channeled through the center of the YaaD barrel to the putative YaaD active site.
-
-	Three-dimensional structure of YaaE from Bacillus subtilis, a glutaminase implicated in pyridoxal-5'-phosphate biosynthesis.,Bauer JA, Bennett EM, Begley TP, Ealick SE J Biol Chem. 2004 Jan 23;279(4):2704-11. Epub 2003 Oct 28. PMID:14585832<ref>PMID:14585832</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1r9g" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bauer~~, J A~~]]	+	[[Category: Bauer JA]]
-	[[Category: Begley~~, T P~~]]	+	[[Category: Begley TP]]
-	[[Category: Bennett~~, E M~~]]	+	[[Category: Bennett EM]]
-	[[Category: Ealick~~, S E]]~~	+	[[Category: Ealick SE]]
-	~~[[Category: Alpha/beta protein]]~~	+
-	~~[[Category: Cofactor biosynthesis]]~~	+
-	~~[[Category: Glutaminase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Triad amidotransferase~~]]	+

OCA at 13:21, 16 December 2020

OCA — Wed, 16 Dec 2020 13:21:50 GMT

←Older revision		Revision as of 13:21, 16 December 2020
Line 1:		Line 1:

	==Three-dimensional Structure of YaaE from Bacillus subtilis==		==Three-dimensional Structure of YaaE from Bacillus subtilis==
-	<StructureSection load='1r9g' size='340' side='right' caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1r9g' size='340' side='right'caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1R9G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1R9G FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YAAE, BSU00120 ([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">YAAE, BSU00120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://pdbe.org/1r9g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9g 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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://pdbe.org/1r9g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Bauer, J A]]		[[Category: Bauer, J A]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 07:34, 28 February 2018

OCA — Wed, 28 Feb 2018 07:34:59 GMT

←Older revision		Revision as of 07:34, 28 February 2018
Line 1:		Line 1:
		+
	==Three-dimensional Structure of YaaE from Bacillus subtilis==		==Three-dimensional Structure of YaaE from Bacillus subtilis==
	<StructureSection load='1r9g' size='340' side='right' caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1r9g' size='340' side='right' caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R9G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R9G FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YAAE, BSU00120 ([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">YAAE, BSU00120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://pdbe.org/1r9g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g 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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://pdbe.org/1r9g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r9/1r9g_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r9/1r9g_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>
	</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=1r9g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Bauer, J A]]		[[Category: Bauer, J A]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 15:00, 11 September 2015

OCA — Fri, 11 Sep 2015 15:00:39 GMT

←Older revision		Revision as of 15:00, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1r9g' size='340' side='right' caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1r9g' size='340' side='right' caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R9G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R9G FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YAAE, BSU00120 ([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">YAAE, BSU00120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g 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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://pdbe.org/1r9g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1r9g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Bauer, J A]]		[[Category: Bauer, J A]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 18:04, 25 December 2014

OCA — Thu, 25 Dec 2014 18:04:52 GMT

←Older revision		Revision as of 18:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R9G FirstGlance]. <br>		<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R9G FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YAAE, BSU00120 ([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">YAAE, BSU00120 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g 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=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDXT_BACSU PDXT_BACSU]] Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Bauer, J A.]]	+	[[Category: Bauer, J A]]
-	[[Category: Begley, T P.]]	+	[[Category: Begley, T P]]
-	[[Category: Bennett, E M.]]	+	[[Category: Bennett, E M]]
-	[[Category: Ealick, S E.]]	+	[[Category: Ealick, S E]]
	[[Category: Alpha/beta protein]]		[[Category: Alpha/beta protein]]
	[[Category: Cofactor biosynthesis]]		[[Category: Cofactor biosynthesis]]

OCA at 16:47, 29 September 2014

OCA — Mon, 29 Sep 2014 16:47:36 GMT

←Older revision		Revision as of 16:47, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1r9g.~~png~~\|~~left~~\|200px]]	+	==Three-dimensional Structure of YaaE from Bacillus subtilis==
		+	<StructureSection load='1r9g' size='340' side='right' caption='[[1r9g]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1r9g]] 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=1R9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R9G FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YAAE, BSU00120 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r9g RCSB], [http://www.ebi.ac.uk/pdbsum/1r9g 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/r9/1r9g_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 ==
		+	The structure of YaaE from Bacillus subtilis was determined at 2.5-A resolution. YaaE is a member of the triad glutamine aminotransferase family and functions in a recently identified alternate pathway for the biosynthesis of vitamin B(6). Proposed active residues include conserved Cys-79, His-170, and Glu-172. YaaE shows similarity to HisH, a glutaminase involved in histidine biosynthesis. YaaD associates with YaaE. A homology model of this protein was constructed. YaaD is predicted to be a (beta/alpha)(8) barrel on the basis of sequence comparisons. The predicted active site includes highly conserved residues 211-216 and 233-235. Finally, a homology model of a putative YaaD-YaaE complex was prepared using the structure of HisH-F as a model. This model predicts that the ammonia molecule generated by YaaE is channeled through the center of the YaaD barrel to the putative YaaD active site.

-	~~{{STRUCTURE_1r9g\| PDB=1r9g \| SCENE= }}~~	+	Three-dimensional structure of YaaE from Bacillus subtilis, a glutaminase implicated in pyridoxal-5'-phosphate biosynthesis.,Bauer JA, Bennett EM, Begley TP, Ealick SE J Biol Chem. 2004 Jan 23;279(4):2704-11. Epub 2003 Oct 28. PMID:14585832<ref>PMID:14585832</ref>

-	~~===Three-dimensional Structure~~ of ~~YaaE from Bacillus subtilis===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14585832}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1r9g]] 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=1R9G OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:014585832<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Bauer, J A.]]		[[Category: Bauer, J A.]]

OCA: Protected "1r9g" [edit=sysop:move=sysop]

OCA — Fri, 04 Jan 2013 10:00:45 GMT

Protected "1r9g" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:00, 4 January 2013

OCA at 10:00, 4 January 2013

OCA — Fri, 04 Jan 2013 10:00:40 GMT

←Older revision		Revision as of 10:00, 4 January 2013
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-	{{Seed}}
	[[Image:1r9g.png\|left\|200px]]		[[Image:1r9g.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1r9g", 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_1r9g\| PDB=1r9g \| SCENE= }}		{{STRUCTURE_1r9g\| PDB=1r9g \| SCENE= }}

	===Three-dimensional Structure of YaaE from Bacillus subtilis===		===Three-dimensional Structure of YaaE from Bacillus subtilis===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14585832}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14585832 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14585832}}		{{ABSTRACT_PUBMED_14585832}}

	==About this Structure==		==About this Structure==
-	~~1R9G~~ 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=1R9G OCA].	+	[[1r9g]] 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=1R9G OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14585832~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014585832</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Bauer, J A.]]		[[Category: Bauer, J A.]]
Line 32:		Line 20:
	[[Category: Cofactor biosynthesis]]		[[Category: Cofactor biosynthesis]]
	[[Category: Glutaminase]]		[[Category: Glutaminase]]
		+	[[Category: Transferase]]
	[[Category: Triad amidotransferase]]		[[Category: Triad amidotransferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:00:17 2009''

OCA at 23:00, 17 February 2009

OCA — Tue, 17 Feb 2009 23:00:20 GMT

←Older revision		Revision as of 23:00, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1R9G is a ~~[[Single protein]]~~ structure of ~~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=1R9G OCA].	+	1R9G 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=1R9G OCA].

	==Reference==		==Reference==
-	Three-dimensional structure of YaaE from Bacillus subtilis, a glutaminase implicated in pyridoxal-5'-phosphate biosynthesis., Bauer JA, Bennett EM, Begley TP, Ealick SE, J Biol Chem. 2004 Jan 23;279(4):2704-11. Epub 2003 Oct 28. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/14585832 14585832]~~	+	<ref group="xtra">PMID:14585832</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Single protein]]
	[[Category: Bauer, J A.]]		[[Category: Bauer, J A.]]
	[[Category: Begley, T P.]]		[[Category: Begley, T P.]]
Line 35:		Line 34:
	[[Category: Triad amidotransferase]]		[[Category: Triad amidotransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 08~~:28:~~28 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:00:17 2009''

OCA at 05:28, 29 July 2008

OCA — Tue, 29 Jul 2008 05:28:35 GMT

←Older revision		Revision as of 05:28, 29 July 2008
Line 1:		Line 1:
-	[[Image:1r9g.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1r9g.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1r9g\| PDB=1r9g \| SCENE= }}		{{STRUCTURE_1r9g\| PDB=1r9g \| SCENE= }}

-	~~'''~~Three-dimensional Structure of YaaE from Bacillus subtilis~~'''~~	+	===Three-dimensional Structure of YaaE from Bacillus subtilis===


-	~~==Overview==~~	+	<!--
-	The ~~structure of YaaE from Bacillus subtilis was determined at 2.5-A resolution. YaaE is a member of~~ the ~~triad glutamine aminotransferase family and functions in a recently identified alternate pathway for~~ the ~~biosynthesis of vitamin B~~(6). ~~Proposed active residues include conserved Cys-79, His-170, and Glu-172~~. ~~YaaE shows similarity to HisH~~, ~~a glutaminase involved in histidine biosynthesis. YaaD associates with YaaE. A homology model of this protein was constructed. YaaD~~ is ~~predicted to be a (beta/alpha)(8) barrel on~~ the ~~basis of sequence comparisons~~. ~~The predicted active site includes highly conserved residues 211~~-~~216 and 233~~-235. Finally, a homology model of a putative YaaD-YaaE complex was prepared using the structure of HisH-F as a model. This model predicts that the ammonia molecule generated by YaaE is channeled through the center of the YaaD barrel to the putative YaaD active site.	+	The line below this paragraph, {{ABSTRACT_PUBMED_14585832}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 14585832 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_14585832}}

	==About this Structure==		==About this Structure==
Line 30:		Line 34:
	[[Category: Glutaminase]]		[[Category: Glutaminase]]
	[[Category: Triad amidotransferase]]		[[Category: Triad amidotransferase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 07~~:14:16 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:28:28 2008''