3cev: Difference between revisions

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-{{Seed}}
-[[Image:3cev.png|left|200px]]
-<!--
+==ARGINASE FROM BACILLUS CALDEVELOX, COMPLEXED WITH L-ARGININE==
-The line below this paragraph, containing "STRUCTURE_3cev", creates the "Structure Box" on the page.
+<StructureSection load='3cev' size='340' side='right'caption='[[3cev]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3cev]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_caldovelox Bacillus caldovelox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CEV FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-{{STRUCTURE_3cev|  PDB=3cev  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cev OCA], [https://pdbe.org/3cev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cev RCSB], [https://www.ebi.ac.uk/pdbsum/3cev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cev ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ARGI_BACCD ARGI_BACCD] Controls arginine catabolism.
+== 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/ce/3cev_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=3cev ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Arginase is a manganese-dependent enzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea. In ureotelic animals arginase is the final enzyme of the urea cycle, but in many species it has a wider role controlling the use of arginine for other metabolic purposes, including the production of creatine, polyamines, proline and nitric oxide. Arginase activity is regulated by various small molecules, including the product L-ornithine. The aim of these structural studies was to test aspects of the catalytic mechanism and to investigate the structural basis of arginase inhibition. RESULTS: We report here the crystal structures of arginase from Bacillus caldovelox at pH 5.6 and pH 8.5, and of binary complexes of the enzyme with L-arginine, L-ornithine and L-lysine at pH 8.5. The arginase monomer comprises a single compact alpha/beta domain that further associates into a hexameric quaternary structure. The binary complexes reveal a common mode of ligand binding, which places the substrate adjacent to the dimanganese centre. We also observe a conformational change that impacts on the active site and is coupled with the occupancy of an external site by guanidine or arginine. CONCLUSIONS: The structures reported here clarify aspects of the active site and indicate key features of the catalytic mechanism, including substrate coordination to one of the manganese ions and an orientational role for a neighboring histidine residue. Stereospecificity for L-amino acids is found to depend on their precise recognition at the active-site rim. Identification of a second arginine-binding site, remote from the active site, and associated conformational changes lead us to propose a regulatory role for this site in substrate hydrolysis.
-===ARGINASE FROM BACILLUS CALDEVELOX, COMPLEXED WITH L-ARGININE===
+Crystal structures of Bacillus caldovelox arginase in complex with substrate and inhibitors reveal new insights into activation, inhibition and catalysis in the arginase superfamily.,Bewley MC, Jeffrey PD, Patchett ML, Kanyo ZF, Baker EN Structure. 1999 Apr 15;7(4):435-48. PMID:10196128<ref>PMID:10196128</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3cev" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10196128}}, adds the Publication Abstract to the page
+*[[Arginase 3D structures|Arginase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10196128 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10196128}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CEV is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_caldovelox Bacillus caldovelox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CEV OCA].
+[[Category: Baker EN]]
+[[Category: Bewley MC]]
-==Reference==
+[[Category: Jeffrey PD]]
-<ref group="xtra">PMID:10196128</ref><references group="xtra"/>
+[[Category: Kanyo ZF]]
-[[Category: Arginase]]
+[[Category: Patchett ML]]
-[[Category: Bacillus caldovelox]]
-[[Category: Baker, E N.]]
-[[Category: Bewley, M C.]]
-[[Category: Jeffrey, P D.]]
-[[Category: Kanyo, Z F.]]
-[[Category: Patchett, M L.]]
-[[Category: Arginine hydrolysis]]
-[[Category: Enzyme]]
-[[Category: Hydrolase]]
-[[Category: Manganese metalloenzyme]]
-[[Category: Nitrogen metabolism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:32:52 2009''