1t4p - Revision history

OCA at 08:36, 14 February 2024

OCA — Wed, 14 Feb 2024 08:36:00 GMT

←Older revision		Revision as of 08:36, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1t4p' size='340' side='right'caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1t4p' size='340' side='right'caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1T4P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T4P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=2BH:[(1E,5S)~~-~~5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=10116 Buffalo rat~~])~~</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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [https://pdbe.org/1t4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [https://www.ebi.ac.uk/pdbsum/1t4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4p ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1]~~ </~~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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [~~http~~://pdbe.org/1t4p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t4p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4p ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ARGI1_RAT ARGI1_RAT]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1t4p 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=1t4p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Arginase is a manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to form L-ornithine and urea. The structure and stability of the binuclear manganese cluster are critical for catalytic activity as it activates the catalytic nucleophile, metal-bridging hydroxide ion, and stabilizes the tetrahedral intermediate and its flanking states. Here, we report X-ray structures of a series of inhibitors bound to the active site of arginase, and each inhibitor exploits a different mode of coordination with the Mn(2+)(2) cluster. Specifically, we have studied the binding of fluoride ion (F(-); an uncompetitive inhibitor) and L-arginine, L-valine, dinor-N(omega)-hydroxy-L-arginine, descarboxy-nor-N(omega)-hydroxy-L-arginine, and dehydro-2(S)-amino-6-boronohexanoic acid. Some inhibitors, such as fluoride ion, dinor-N(omega)-hydroxy-L-arginine, and dehydro-2(S)-amino-6-boronohexanoic acid, cause the net addition of one ligand to the Mn(2+)(2) cluster. Other inhibitors, such as descarboxy-nor-N(omega)-hydroxy-L-arginine, simply displace the metal-bridging hydroxide ion of the native enzyme and do not cause any net change in the metal coordination polyhedra. The highest affinity inhibitors displace the metal-bridging hydroxide ion (and sometimes occupy a Mn(2+)(A) site found vacant in the native enzyme) and maintain a conserved array of hydrogen bonds with their alpha-amino and -carboxylate groups.
-
-	Inhibitor coordination interactions in the binuclear manganese cluster of arginase.,Cama E, Pethe S, Boucher JL, Han S, Emig FA, Ash DE, Viola RE, Mansuy D, Christianson DW Biochemistry. 2004 Jul 20;43(28):8987-99. PMID:15248756<ref>PMID:15248756</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1t4p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Arginase 3D structures\|Arginase 3D structures]]		*[[Arginase 3D structures\|Arginase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arginase]]
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ash~~, D E~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Boucher, J L]]	+	[[Category: Ash DE]]
-	[[Category: Cama, E]]	+	[[Category: Boucher J-L]]
-	[[Category: Christianson~~, D W~~]]	+	[[Category: Cama E]]
-	[[Category: Emig~~, F A~~]]	+	[[Category: Christianson DW]]
-	[[Category: Han, S]]	+	[[Category: Emig FA]]
-	[[Category: Mansuy, D]]	+	[[Category: Han S]]
-	[[Category: Pethe, S]]	+	[[Category: Mansuy D]]
-	[[Category: Viola~~, R E]]~~	+	[[Category: Pethe S]]
-	~~[[Category: Dehydro-abh]]~~	+	[[Category: Viola RE]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:42, 24 December 2020

OCA — Thu, 24 Dec 2020 11:42:27 GMT

←Older revision		Revision as of 11:42, 24 December 2020
Line 1:		Line 1:

	==Arginase-dehydro-ABH complex==		==Arginase-dehydro-ABH complex==
-	<StructureSection load='1t4p' size='340' side='right' caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='1t4p' size='340' side='right'caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T4P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T4P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://pdbe.org/1t4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4p 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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://pdbe.org/1t4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4p ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Arginase\|Arginase]]	+	*[[Arginase 3D structures\|Arginase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	[[Category: Arginase]]		[[Category: Arginase]]
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Ash, D E]]		[[Category: Ash, D E]]
	[[Category: Boucher, J L]]		[[Category: Boucher, J L]]

OCA at 08:01, 14 March 2018

OCA — Wed, 14 Mar 2018 08:01:49 GMT

←Older revision		Revision as of 08:01, 14 March 2018
Line 1:		Line 1:
		+
	==Arginase-dehydro-ABH complex==		==Arginase-dehydro-ABH complex==
	<StructureSection load='1t4p' size='340' side='right' caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1t4p' size='340' side='right' caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://pdbe.org/1t4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p 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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://pdbe.org/1t4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t4p ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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/t4/1t4p_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t4/1t4p_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=1t4p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:04, 11 September 2015

OCA — Fri, 11 Sep 2015 08:04:39 GMT

←Older revision		Revision as of 08:04, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1t4p' size='340' side='right' caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1t4p' size='340' side='right' caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 ~~Rattus norvegicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p 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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://pdbe.org/1t4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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 1t4p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Arginase]]		[[Category: Arginase]]
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Ash, D E]]		[[Category: Ash, D E]]
	[[Category: Boucher, J L]]		[[Category: Boucher, J L]]

OCA at 07:29, 6 January 2015

OCA — Tue, 06 Jan 2015 07:29:02 GMT

←Older revision		Revision as of 07:29, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4P FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p 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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Arginase]]		[[Category: Arginase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Ash, D E.]]	+	[[Category: Ash, D E]]
-	[[Category: Boucher, J L.]]	+	[[Category: Boucher, J L]]
-	[[Category: Cama, E.]]	+	[[Category: Cama, E]]
-	[[Category: Christianson, D W.]]	+	[[Category: Christianson, D W]]
-	[[Category: Emig, F A.]]	+	[[Category: Emig, F A]]
-	[[Category: Han, S.]]	+	[[Category: Han, S]]
-	[[Category: Mansuy, D.]]	+	[[Category: Mansuy, D]]
-	[[Category: Pethe, S.]]	+	[[Category: Pethe, S]]
-	[[Category: Viola, R E~~.]]~~	+	[[Category: Viola, R E]]
-	~~[[Category: Arginase~~]]	+
	[[Category: Dehydro-abh]]		[[Category: Dehydro-abh]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 20:41, 29 September 2014

OCA — Mon, 29 Sep 2014 20:41:32 GMT

←Older revision		Revision as of 20:41, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1t4p.~~png~~\|~~left~~\|200px]]	+	==Arginase-dehydro-ABH complex==
		+	<StructureSection load='1t4p' size='340' side='right' caption='[[1t4p]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T4P FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BH:[(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-)'>2BH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d3v\|1d3v]], [[1t4r\|1t4r]], [[1t4s\|1t4s]], [[1t4t\|1t4t]], [[1t5f\|1t5f]], [[1t5g\|1t5g]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] </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=1t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t4p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t4p RCSB], [http://www.ebi.ac.uk/pdbsum/1t4p 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/t4/1t4p_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 ==
		+	Arginase is a manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to form L-ornithine and urea. The structure and stability of the binuclear manganese cluster are critical for catalytic activity as it activates the catalytic nucleophile, metal-bridging hydroxide ion, and stabilizes the tetrahedral intermediate and its flanking states. Here, we report X-ray structures of a series of inhibitors bound to the active site of arginase, and each inhibitor exploits a different mode of coordination with the Mn(2+)(2) cluster. Specifically, we have studied the binding of fluoride ion (F(-); an uncompetitive inhibitor) and L-arginine, L-valine, dinor-N(omega)-hydroxy-L-arginine, descarboxy-nor-N(omega)-hydroxy-L-arginine, and dehydro-2(S)-amino-6-boronohexanoic acid. Some inhibitors, such as fluoride ion, dinor-N(omega)-hydroxy-L-arginine, and dehydro-2(S)-amino-6-boronohexanoic acid, cause the net addition of one ligand to the Mn(2+)(2) cluster. Other inhibitors, such as descarboxy-nor-N(omega)-hydroxy-L-arginine, simply displace the metal-bridging hydroxide ion of the native enzyme and do not cause any net change in the metal coordination polyhedra. The highest affinity inhibitors displace the metal-bridging hydroxide ion (and sometimes occupy a Mn(2+)(A) site found vacant in the native enzyme) and maintain a conserved array of hydrogen bonds with their alpha-amino and -carboxylate groups.

-	~~{{STRUCTURE_1t4p\| PDB=1t4p \| SCENE= }}~~	+	Inhibitor coordination interactions in the binuclear manganese cluster of arginase.,Cama E, Pethe S, Boucher JL, Han S, Emig FA, Ash DE, Viola RE, Mansuy D, Christianson DW Biochemistry. 2004 Jul 20;43(28):8987-99. PMID:15248756<ref>PMID:15248756</ref>

-	~~===Arginase-dehydro-ABH complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15248756}}~~	+	==See Also==
-		+	*[[Arginase\|Arginase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1t4p~~]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015248756<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Arginase]]		[[Category: Arginase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]

OCA: Protected "1t4p" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:30:06 GMT

Protected "1t4p" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:30, 5 January 2013

OCA at 11:30, 5 January 2013

OCA — Sat, 05 Jan 2013 11:30:04 GMT

←Older revision		Revision as of 11:30, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1t4p.png\|left\|200px]]		[[Image:1t4p.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t4p", 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_1t4p\| PDB=1t4p \| SCENE= }}		{{STRUCTURE_1t4p\| PDB=1t4p \| SCENE= }}

	===Arginase-dehydro-ABH complex===		===Arginase-dehydro-ABH complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15248756}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15248756 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15248756}}		{{ABSTRACT_PUBMED_15248756}}

	==About this Structure==		==About this Structure==
-	~~1T4P~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA].	+	[[1t4p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15248756~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015248756</ref><references group="xtra"/>
	[[Category: Arginase]]		[[Category: Arginase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
Line 37:		Line 25:
	[[Category: Arginase]]		[[Category: Arginase]]
	[[Category: Dehydro-abh]]		[[Category: Dehydro-abh]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 17:35:57 2009''~~	+

OCA at 15:35, 17 February 2009

OCA — Tue, 17 Feb 2009 15:35:59 GMT

←Older revision		Revision as of 15:35, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1T4P is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA].	+	1T4P is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T4P OCA].

	==Reference==		==Reference==
-	Inhibitor coordination interactions in the binuclear manganese cluster of arginase., Cama E, Pethe S, Boucher JL, Han S, Emig FA, Ash DE, Viola RE, Mansuy D, Christianson DW, Biochemistry. 2004 Jul 20;43(28):8987-99. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15248756 15248756]~~	+	<ref group="xtra">PMID:15248756</ref><references group="xtra"/>
	[[Category: Arginase]]		[[Category: Arginase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Single protein]]
	[[Category: Ash, D E.]]		[[Category: Ash, D E.]]
	[[Category: Boucher, J L.]]		[[Category: Boucher, J L.]]
Line 39:		Line 38:
	[[Category: Dehydro-abh]]		[[Category: Dehydro-abh]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:36:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:35:57 2009''

OCA at 21:36, 28 July 2008

OCA — Mon, 28 Jul 2008 21:36:29 GMT

←Older revision		Revision as of 21:36, 28 July 2008
Line 1:		Line 1:
-	[[Image:1t4p.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1t4p.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1t4p\| PDB=1t4p \| SCENE= }}		{{STRUCTURE_1t4p\| PDB=1t4p \| SCENE= }}

-	~~'''~~Arginase-dehydro-ABH complex~~'''~~	+	===Arginase-dehydro-ABH complex===


-	~~==Overview==~~	+	<!--
-	~~Arginase is a manganese metalloenzyme that catalyzes the hydrolysis of L~~-~~arginine to form L~~-~~ornithine and urea.~~ The ~~structure and stability of the binuclear manganese cluster are critical for catalytic activity as it activates the catalytic nucleophile~~, ~~metal-bridging hydroxide ion~~, ~~and stabilizes~~ the ~~tetrahedral intermediate and its flanking states. Here, we report X-ray structures of a series of inhibitors bound~~ to the ~~active site of arginase, and each inhibitor exploits a different mode of coordination with the Mn~~(~~2+)(2) cluster~~. Specifically, we have studied the binding of fluoride ion (F(-); an uncompetitive inhibitor) and L-arginine, L-valine, dinor-N(omega)-hydroxy-L-arginine, descarboxy-nor-N(omega)-hydroxy-L-arginine, and dehydro-2(S)-amino-6-boronohexanoic acid. ~~Some inhibitors, such as fluoride ion, dinor-N(omega~~)~~-hydroxy-L-arginine~~, ~~and dehydro-2(S)-amino-6-boronohexanoic acid, cause~~ the ~~net addition of one ligand to the Mn(2+)(2) cluster~~. ~~Other inhibitors, such as descarboxy~~-~~nor~~-N(omega)-hydroxy-L-arginine, simply displace the metal-bridging hydroxide ion of the native enzyme and do not cause any net change in the metal coordination polyhedra. The highest affinity inhibitors displace the metal-bridging hydroxide ion (and sometimes occupy a Mn(2+)(A) site found vacant in the native enzyme) and maintain a conserved array of hydrogen bonds with their alpha-amino and -carboxylate groups.	+	The line below this paragraph, {{ABSTRACT_PUBMED_15248756}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15248756 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15248756}}

	==About this Structure==		==About this Structure==
Line 34:		Line 38:
	[[Category: Arginase]]		[[Category: Arginase]]
	[[Category: Dehydro-abh]]		[[Category: Dehydro-abh]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 09~~:31:24 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 00:36:20 2008''