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4dr0

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==Crystal structure of Bacillus subtilis dimanganese(II) NrdF==
==Crystal structure of Bacillus subtilis dimanganese(II) NrdF==
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<StructureSection load='4dr0' size='340' side='right' caption='[[4dr0]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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<StructureSection load='4dr0' size='340' side='right'caption='[[4dr0]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4dr0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DR0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DR0 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4dr0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DR0 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU17390, nrdF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr><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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr0 OCA], [https://pdbe.org/4dr0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dr0 RCSB], [https://www.ebi.ac.uk/pdbsum/4dr0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr0 ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dr0 RCSB], [http://www.ebi.ac.uk/pdbsum/4dr0 PDBsum]</span></td></tr>
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</table>
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<table>
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== Function ==
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<div style="background-color:#fffaf0;">
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[https://www.uniprot.org/uniprot/RIR2_BACSU RIR2_BACSU] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).
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== Publication Abstract from PubMed ==
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Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn&lt;sup&gt;III&lt;/sup&gt;&lt;sub&gt;2&lt;/sub&gt;-Y*, in their homodimeric NrdF (beta2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn&lt;sup&gt;II&lt;/sup&gt;&lt;sub&gt;2&lt;/sub&gt; form of NrdF is an important component in understanding O&lt;sub&gt;2&lt;/sub&gt; -mediated formation of the active metallocofactor, a subject of much interest since a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of &lt;i&gt;Escherichia coli&lt;/i&gt; Mn&lt;sup&gt;II&lt;/sup&gt;&lt;sub&gt;2&lt;/sub&gt;-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 A resolution crystal structure of &lt;i&gt;Bacillus subtilis&lt;/i&gt; Mn&lt;sup&gt;II&lt;/sup&gt;&lt;sub&gt;2&lt;/sub&gt;-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus genera. The structures of the metal clusters in the beta2 dimer are distinct from those observed in &lt;i&gt;E. coli&lt;/i&gt; Mn&lt;sup&gt;II&lt;/sup&gt;&lt;sub&gt;2&lt;/sub&gt;-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn&lt;sup&gt;II&lt;/sup&gt;&lt;sub&gt;2&lt;/sub&gt; cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn&lt;sup&gt;III&lt;/sup&gt;&lt;sub&gt;2&lt;/sub&gt;-Y* cofactor assembly in class Ib RNRs.
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The dimanganese(II) site in &lt;i&gt;Bacillus subtilis&lt;/i&gt; class Ib ribonucleotide reductase.,Boal AK, Cotruvo JA, Stubbe J, Rosenzweig AC Biochemistry. 2012 Mar 23. PMID:22443445<ref>PMID:22443445</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[Ribonucleotide reductase|Ribonucleotide reductase]]
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*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Ribonucleoside-diphosphate reductase]]
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[[Category: Large Structures]]
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[[Category: Boal, A K.]]
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[[Category: Boal AK]]
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[[Category: Cotruvo, J A.]]
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[[Category: Cotruvo Jr JA]]
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[[Category: Rosenzweig, A C.]]
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[[Category: Rosenzweig AC]]
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[[Category: Stubbe, J.]]
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[[Category: Stubbe J]]
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[[Category: Manganese]]
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[[Category: Oxidoreductase]]
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[[Category: Ribonucleotide reductase]]
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Current revision

Crystal structure of Bacillus subtilis dimanganese(II) NrdF

PDB ID 4dr0

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