4r7g - Revision history

OCA at 15:12, 8 November 2023

OCA — Wed, 08 Nov 2023 15:12:44 GMT

←Older revision		Revision as of 15:12, 8 November 2023
Line 1:		Line 1:

	==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==		==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==
-	<StructureSection load='4r7g' size='340' side='right'caption='[[4r7g]]' scene=''>	+	<StructureSection load='4r7g' size='340' side='right'caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' 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=4R7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4r7g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R7G 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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [https://pdbe.org/4r7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [https://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</span></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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [https://pdbe.org/4r7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [https://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PUR4_SALTY PUR4_SALTY]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Molecular tunnels in enzyme systems possess variable architecture and are therefore difficult to predict. In this work, we design and apply an algorithm to resolve the pathway followed by ammonia using the bifunctional enzyme formylglycinamide ribonucleotide amidotransferase (FGAR-AT) as a model system. Though its crystal structure has been determined, an ammonia pathway connecting the glutaminase domain to the 30 A distal FGAR/ATP binding site remains elusive. Crystallography suggested two purported paths: an N-terminal-adjacent path (path 1) and an auxiliary ADP-adjacent path (path 2). The algorithm presented here, RismPath, which enables fast and accurate determination of solvent distribution inside a protein channel, predicted path 2 as the preferred mode of ammonia transfer. Supporting experimental studies validate the identity of the path, and results lead to the conclusion that the residues in the middle of the channel do not partake in catalytic coupling and serve only as channel walls facilitating ammonia transfer.
		+
		+	Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway by Combining 3D-RISM Theory with Experiment.,Tanwar AS, Sindhikara DJ, Hirata F, Anand R ACS Chem Biol. 2015 Jan 14. PMID:25551173<ref>PMID:25551173</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4r7g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
	[[Category: Anand R]]		[[Category: Anand R]]
	[[Category: Hirata F]]		[[Category: Hirata F]]
	[[Category: Sindhikara DJ]]		[[Category: Sindhikara DJ]]
	[[Category: Tanwar AS]]		[[Category: Tanwar AS]]

OCA at 10:57, 31 August 2022

OCA — Wed, 31 Aug 2022 10:57:52 GMT

←Older revision		Revision as of 10:57, 31 August 2022
Line 1:		Line 1:

	==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==		==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==
-	<StructureSection load='4r7g' size='340' side='right'caption='[[4r7g]]~~, [[Resolution\|resolution]] 2.90Å~~' scene=''>	+	<StructureSection load='4r7g' size='340' side='right'caption='[[4r7g]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[4r7g]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [https://pdbe.org/4r7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [https://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</span></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</scene></td></tr>	+
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t3t\|1t3t]]</div></td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [https://pdbe.org/4r7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [https://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Molecular tunnels in enzyme systems possess variable architecture and are therefore difficult to predict. In this work, we design and apply an algorithm to resolve the pathway followed by ammonia using the bifunctional enzyme formylglycinamide ribonucleotide amidotransferase (FGAR-AT) as a model system. Though its crystal structure has been determined, an ammonia pathway connecting the glutaminase domain to the 30 A distal FGAR/ATP binding site remains elusive. Crystallography suggested two purported paths: an N-terminal-adjacent path (path 1) and an auxiliary ADP-adjacent path (path 2). The algorithm presented here, RismPath, which enables fast and accurate determination of solvent distribution inside a protein channel, predicted path 2 as the preferred mode of ammonia transfer. Supporting experimental studies validate the identity of the path, and results lead to the conclusion that the residues in the middle of the channel do not partake in catalytic coupling and serve only as channel walls facilitating ammonia transfer.
-
-	Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway by Combining 3D-RISM Theory with Experiment.,Tanwar AS, Sindhikara DJ, Hirata F, Anand R ACS Chem Biol. 2015 Jan 14. PMID:25551173<ref>PMID:25551173</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4r7g" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Phosphoribosylformylglycinamidine synthase]]~~	+	[[Category: Anand R]]
-	[[Category: Anand, R]]	+	[[Category: Hirata F]]
-	[[Category: Hirata, F]]	+	[[Category: Sindhikara DJ]]
-	[[Category: Sindhikara~~, D J~~]]	+	[[Category: Tanwar AS]]
-	[[Category: Tanwar~~, A S]]~~	+
-	~~[[Category: Amidotransferase]]~~	+
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Gene duplication]]~~	+
-	~~[[Category: Ligase~~]]	+

OCA at 05:08, 25 August 2022

OCA — Thu, 25 Aug 2022 05:08:15 GMT

←Older revision		Revision as of 05:08, 25 August 2022
Line 1:		Line 1:

	==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==		==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==
-	<StructureSection load='4r7g' size='340' side='right' caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='4r7g' size='340' side='right'caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4r7g]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Salty Salty]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4R7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4r7g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">~~[[1t3t\|1t3t]]~~<~~/td></tr>~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t3t\|1t3t]]</div></td></tr>
-	~~<tr id~~='~~gene~~'~~><td class="sblockLbl"><b~~>[[~~Gene~~\|~~Gene:~~]]</b>~~</td><td class="sblockDat">purL, STM2565 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])~~</td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [https://pdbe.org/4r7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [https://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [~~http~~://pdbe.org/4r7g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phosphoribosylformylglycinamidine synthase]]		[[Category: Phosphoribosylformylglycinamidine synthase]]
-	[[Category: Salty]]
	[[Category: Anand, R]]		[[Category: Anand, R]]
	[[Category: Hirata, F]]		[[Category: Hirata, F]]

OCA at 09:02, 22 November 2017

OCA — Wed, 22 Nov 2017 09:02:16 GMT

←Older revision		Revision as of 09:02, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4r7g' size='340' side='right' caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4r7g' size='340' side='right' caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4r7g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4r7g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R7G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3t\|1t3t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3t\|1t3t]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purL, STM2565 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [http://pdbe.org/4r7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [http://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [http://pdbe.org/4r7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [http://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</span></td></tr>
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Phosphoribosylformylglycinamidine synthase]]		[[Category: Phosphoribosylformylglycinamidine synthase]]
		+	[[Category: Salty]]
	[[Category: Anand, R]]		[[Category: Anand, R]]
	[[Category: Hirata, F]]		[[Category: Hirata, F]]

OCA at 12:02, 11 August 2016

OCA — Thu, 11 Aug 2016 12:02:25 GMT

←Older revision		Revision as of 12:02, 11 August 2016
Line 1:		Line 1:
		+
	==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==		==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==
	<StructureSection load='4r7g' size='340' side='right' caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4r7g' size='340' side='right' caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3t\|1t3t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3t\|1t3t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [http://www.ebi.ac.uk/pdbsum/4r7g 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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [http://pdbe.org/4r7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [http://www.ebi.ac.uk/pdbsum/4r7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r7g ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4r7g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:50, 21 January 2015

OCA — Wed, 21 Jan 2015 16:50:36 GMT

←Older revision		Revision as of 16:50, 21 January 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment==
		+	<StructureSection load='4r7g' size='340' side='right' caption='[[4r7g]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4r7g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R7G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYG:2-AMINO-4-(AMINO-3-OXO-PROPYLSULFANYLCARBONYL)-BUTYRIC+ACID'>CYG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t3t\|1t3t]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] </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=4r7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4r7g RCSB], [http://www.ebi.ac.uk/pdbsum/4r7g PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Molecular tunnels in enzyme systems possess variable architecture and are therefore difficult to predict. In this work, we design and apply an algorithm to resolve the pathway followed by ammonia using the bifunctional enzyme formylglycinamide ribonucleotide amidotransferase (FGAR-AT) as a model system. Though its crystal structure has been determined, an ammonia pathway connecting the glutaminase domain to the 30 A distal FGAR/ATP binding site remains elusive. Crystallography suggested two purported paths: an N-terminal-adjacent path (path 1) and an auxiliary ADP-adjacent path (path 2). The algorithm presented here, RismPath, which enables fast and accurate determination of solvent distribution inside a protein channel, predicted path 2 as the preferred mode of ammonia transfer. Supporting experimental studies validate the identity of the path, and results lead to the conclusion that the residues in the middle of the channel do not partake in catalytic coupling and serve only as channel walls facilitating ammonia transfer.

-	~~The entry 4r7g is ON HOLD until Paper Publication~~	+	Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway by Combining 3D-RISM Theory with Experiment.,Tanwar AS, Sindhikara DJ, Hirata F, Anand R ACS Chem Biol. 2015 Jan 14. PMID:25551173<ref>PMID:25551173</ref>

-	~~Authors: Tanwar~~, A.S.~~, Sindhikara, D.J., Hirata, F., Anand, R~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: ~~Sindhikara~~, ~~D.J~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Phosphoribosylformylglycinamidine synthase]]
		+	[[Category: Anand, R]]
	[[Category: Hirata, F]]		[[Category: Hirata, F]]
-	[[Category: ~~Anand~~, R]]	+	[[Category: Sindhikara, D J]]
-	[[Category: Tanwar, A.S]]	+	[[Category: Tanwar, A S]]
		+	[[Category: Amidotransferase]]
		+	[[Category: Atp binding]]
		+	[[Category: Gene duplication]]
		+	[[Category: Ligase]]

OCA at 11:45, 31 December 2014

OCA — Wed, 31 Dec 2014 11:45:01 GMT

←Older revision		Revision as of 11:45, 31 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4r7g is ON HOLD	+	The entry 4r7g is ON HOLD until Paper Publication

	Authors: Tanwar, A.S., Sindhikara, D.J., Hirata, F., Anand, R.		Authors: Tanwar, A.S., Sindhikara, D.J., Hirata, F., Anand, R.

OCA at 16:35, 24 December 2014

OCA — Wed, 24 Dec 2014 16:35:42 GMT

←Older revision		Revision as of 16:35, 24 December 2014
Line 6:		Line 6:

	Description: Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment		Description: Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment
		+	[[Category: Unreleased Structures]]
		+	[[Category: Sindhikara, D.J]]
		+	[[Category: Hirata, F]]
		+	[[Category: Anand, R]]
		+	[[Category: Tanwar, A.S]]

OCA at 23:06, 1 October 2014

OCA — Wed, 01 Oct 2014 23:06:57 GMT

←Older revision		Revision as of 23:06, 1 October 2014
Line 3:		Line 3:
	The entry 4r7g is ON HOLD		The entry 4r7g is ON HOLD

-	Authors: Tanwar, A. S., Sindhikara, D.J., Hirata, F., Anand, R.	+	Authors: Tanwar, A.S., Sindhikara, D.J., Hirata, F., Anand, R.

	Description: Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment		Description: Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment

OCA: Protected "4r7g" [edit=sysop:move=sysop]

OCA — Thu, 04 Sep 2014 04:19:00 GMT

Protected "4r7g" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:19, 4 September 2014