3n3b: Difference between revisions
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==Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide== | |||
<StructureSection load='3n3b' size='340' side='right'caption='[[3n3b]], [[Resolution|resolution]] 2.36Å' scene=''> | |||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.36Å</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> | |||
<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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3n3b" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Ribonucleotide reductase|Ribonucleotide reductase]] | *[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: Escherichia coli]] | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: Boal | [[Category: Large Structures]] | ||
[[Category: Cotruvo | [[Category: Boal AK]] | ||
[[Category: Rosenzweig | [[Category: Cotruvo Jr JA]] | ||
[[Category: Stubbe | [[Category: Rosenzweig AC]] | ||
[[Category: Stubbe J]] | |||
Latest revision as of 12:07, 6 September 2023
Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped PeroxideRibonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide
Structural highlights
FunctionRIR4_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 Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. Structural Basis for Activation of Class Ib Ribonucleotide Reductase.,Boal AK, Cotruvo JA Jr, Stubbe J, Rosenzweig AC Science. 2010 Aug 5. PMID:20688982[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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