6mw3: Difference between revisions

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 ==EM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha subunit and NrdF beta subunit with dATP==
-<StructureSection load='6mw3' size='340' side='right'caption='[[6mw3]], [[Resolution|resolution]] 4.65&Aring;' scene=''>
+<SX load='6mw3' size='340' side='right' viewer='molstar' caption='[[6mw3]], [[Resolution|resolution]] 4.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6mw3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MW3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6mw3]] is a 4 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=6MW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MW3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.65&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6mt9|6mt9]], [[6mve|6mve]], [[6mv9|6mv9]], [[6myx|6myx]]</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=6mw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mw3 OCA], [https://pdbe.org/6mw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mw3 RCSB], [https://www.ebi.ac.uk/pdbsum/6mw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mw3 ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6mw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mw3 OCA], [http://pdbe.org/6mw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mw3 RCSB], [http://www.ebi.ac.uk/pdbsum/6mw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mw3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/A0A162Q3J9_BACIU A0A162Q3J9_BACIU]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410]
+[https://www.uniprot.org/uniprot/RIR1_BACSU RIR1_BACSU] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.
-Convergent allostery in ribonucleotide reductase.,Thomas WC, Brooks FP 3rd, Burnim AA, Bacik JP, Stubbe J, Kaelber JT, Chen JZ, Ando N Nat Commun. 2019 Jun 14;10(1):2653. doi: 10.1038/s41467-019-10568-4. PMID:31201319<ref>PMID:31201319</ref>
+==See Also==
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6mw3" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
-</StructureSection>
+</SX>
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Ribonucleoside-diphosphate reductase]]
+[[Category: Ando N]]
-[[Category: Ando, N]]
+[[Category: Bacik JP]]
-[[Category: Bacik, J P]]
+[[Category: Kaelber JT]]
-[[Category: Kaelber, J T]]
+[[Category: Thomas WC]]
-[[Category: Thomas, W C]]
-[[Category: Allostery]]
-[[Category: Atp]]
-[[Category: Datp]]
-[[Category: Filament]]
-[[Category: Nucleotide metabolism]]
-[[Category: Oxidoreductase]]
-[[Category: Ribonucleotide reductase]]