3n3b: Difference between revisions

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-{{Seed}}
-[[Image:3n3b.jpg|left|200px]]
-<!--
+==Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide==
-The line below this paragraph, containing "STRUCTURE_3n3b", creates the "Structure Box" on the page.
+<StructureSection load='3n3b' size='340' side='right'caption='[[3n3b]], [[Resolution|resolution]] 2.36&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'>[[3n3b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N3B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N3B 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]] 2.36&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
-{{STRUCTURE_3n3b|  PDB=3n3b  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3n3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n3b OCA], [https://pdbe.org/3n3b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n3b RCSB], [https://www.ebi.ac.uk/pdbsum/3n3b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n3b ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIR4_ECOLI RIR4_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F 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/n3/3n3b_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=3n3b ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)(2)-tyrosyl radical (Y*) or a Fe(III)(2)-Y* cofactor in the NrdF subunit. Whereas Fe(III)(2)-Y* can self-assemble from Fe(II)(2)-NrdF and O(2), activation of Mn(II)(2)-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O(2). The crystal structures reported here of E. coli Mn(II)(2)-NrdF and Fe(II)(2)-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)(2)-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)(2) active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)(2)-Y* cofactor assembly.
-===Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide===
+Structural Basis for Activation of Class Ib Ribonucleotide Reductase.,Boal AK, Cotruvo JA Jr, Stubbe J, Rosenzweig AC Science. 2010 Aug 5. PMID:20688982<ref>PMID:20688982</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3n3b" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20688982}}, adds the Publication Abstract to the page
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20688982 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20688982}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-N3B is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N3B OCA].
+[[Category: Large Structures]]
+[[Category: Boal AK]]
-==Reference==
+[[Category: Cotruvo Jr JA]]
-<ref group="xtra">PMID:20688982</ref><references group="xtra"/>
+[[Category: Rosenzweig AC]]
-[[Category: Escherichia coli]]
+[[Category: Stubbe J]]
-[[Category: Ribonucleoside-diphosphate reductase]]
-[[Category: Boal, A K.]]
-[[Category: Cotruvo, J A.]]
-[[Category: Rosenzweig, A C.]]
-[[Category: Stubbe, J.]]
-[[Category: Dimanganese cluster]]
-[[Category: Flavoprotein]]
-[[Category: Four-helix bundle]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxide]]
-[[Category: Ribonucleotide reductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:47:20 2010''