1jpr: Difference between revisions

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 ==Mn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxide==
-<StructureSection load='1jpr' size='340' side='right' caption='[[1jpr]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
+<StructureSection load='1jpr' size='340' side='right'caption='[[1jpr]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1jpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JPR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1jpr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JPR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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]] 1.88&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jqc|1jqc]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=1jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpr OCA], [https://pdbe.org/1jpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jpr RCSB], [https://www.ebi.ac.uk/pdbsum/1jpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jpr 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=1jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpr OCA], [http://pdbe.org/1jpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jpr RCSB], [http://www.ebi.ac.uk/pdbsum/1jpr PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.
+[https://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.
 == 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/jp/1jpr_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jp/1jpr_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].
+</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=1jpr ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The di-iron carboxylate proteins constitute a diverse class of non-heme iron enzymes performing a multitude of redox reactions. These reactions usually involve high-valent Fe-oxo species and are thought to be controlled by carboxylate shifts. Owing to their short lifetime, the intermediate structures have so far escaped structural characterization by X-ray crystallography. In an attempt to map the carboxylate conformations available to the protein during different redox states and different ligand environments, we have studied metal-substituted forms of the R2 protein of ribonucleotide reductase from Escherichia coli. In the present work we have solved the crystal structures of Mn-substituted R2 oxidized in two different ways. Oxidation was performed using either nitric oxide or a combination of hydrogen peroxide and hydroxylamine. The two structures are virtually identical, indicating that the oxidation states are the same, most likely a mixed-valent MnII-MnIII centre. One of the carboxylate ligands (D84) adopts a new, so far unseen, conformation, which could participate in the mechanism for radical generation in R2. E238 adopts a bridging-chelating conformation proposed to be important for proper O2 activation but not previously observed in the wild-type enzyme. Probable catalase activity was also observed during the oxidation with H2O2, indicating mechanistic similarities to the di-Mn catalases.
-Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation.,Hogbom M, Andersson ME, Nordlund P J Biol Inorg Chem. 2001 Mar;6(3):315-23. PMID:11315567<ref>PMID:11315567</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1jpr" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ribonucleotide reductase|Ribonucleotide reductase]]
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Ribonucleoside-diphosphate reductase]]
+[[Category: Large Structures]]
-[[Category: Andersson, M E]]
+[[Category: Andersson ME]]
-[[Category: Hogbom, M]]
+[[Category: Hogbom M]]
-[[Category: Nordlund, P]]
+[[Category: Nordlund P]]
-[[Category: Mn substituted]]
-[[Category: Oxidized by no]]
-[[Category: Oxidoreductase]]
-[[Category: Radical protein]]