1t5g: Difference between revisions

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-[[Image:1t5g.gif|left|200px]]
- {{Structure
+==Arginase-F2-L-Arginine complex==
-|PDB= 1t5g |SIZE=350|CAPTION= <scene name='initialview01'>1t5g</scene>, resolution 2.40&Aring;
+<StructureSection load='1t5g' size='340' side='right'caption='[[1t5g]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>
+<table><tr><td colspan='2'>[[1t5g]] 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=1T5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T5G FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-|GENE= ARG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t5g OCA], [https://pdbe.org/1t5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t5g RCSB], [https://www.ebi.ac.uk/pdbsum/1t5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t5g ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1t5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t5g OCA], [http://www.ebi.ac.uk/pdbsum/1t5g PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1t5g RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/ARGI1_RAT ARGI1_RAT]
+== 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/t5/1t5g_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/main_output.php?pdb_ID=1t5g ConSurf].
+<div style="clear:both"></div>
-'''Arginase-F2-L-Arginine complex'''
+==See Also==
+*[[Arginase 3D structures|Arginase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-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.
+[[Category: Large Structures]]
-==About this Structure==
-T5G 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=1T5G OCA].
-==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]
-[[Category: Arginase]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Ash DE]]
-[[Category: Ash, D E.]]
+[[Category: Boucher J-L]]
-[[Category: Boucher, J L.]]
+[[Category: Cama E]]
-[[Category: Cama, E.]]
+[[Category: Christianson DW]]
-[[Category: Christianson, D W.]]
+[[Category: Emig FA]]
-[[Category: Emig, F A.]]
+[[Category: Han S]]
-[[Category: Han, S.]]
+[[Category: Mansuy D]]
-[[Category: Mansuy, D.]]
+[[Category: Pethe S]]
-[[Category: Pethe, S.]]
+[[Category: Viola RE]]
-[[Category: Viola, R E.]]
-[[Category: arginase]]
-[[Category: fluoride ion]]
-[[Category: l-arginine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:51:30 2008''