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6myx

From Proteopedia

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Current revision (14:45, 13 March 2024) (edit) (undo)
 
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<SX load='6myx' size='340' side='right' viewer='molstar' caption='[[6myx]], [[Resolution|resolution]] 6.00&Aring;' scene=''>
<SX load='6myx' size='340' side='right' viewer='molstar' caption='[[6myx]], [[Resolution|resolution]] 6.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6myx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MYX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6MYX FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6myx]] 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=6MYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MYX FirstGlance]. <br>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 6&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6mt9|6mt9]], [[6mve|6mve]], [[6mv9|6mv9]]</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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrdE_1, B4417_3413, NCTC3610_03984 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=6myx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myx OCA], [https://pdbe.org/6myx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6myx RCSB], [https://www.ebi.ac.uk/pdbsum/6myx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6myx ProSAT]</span></td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6myx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6myx OCA], [http://pdbe.org/6myx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6myx RCSB], [http://www.ebi.ac.uk/pdbsum/6myx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6myx ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[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]
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[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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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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<div class="pdbe-citations 6myx" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</SX>
</SX>
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[[Category: Vibrio subtilis ehrenberg 1835]]
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[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ribonucleoside-diphosphate reductase]]
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[[Category: Ando N]]
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[[Category: Ando, N]]
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[[Category: Bacik JP]]
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[[Category: Bacik, J P]]
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[[Category: Chen JZ]]
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[[Category: Chen, J Z]]
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[[Category: Thomas WC]]
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[[Category: Thomas, W C]]
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[[Category: Allostery]]
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[[Category: Atp]]
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[[Category: Datp]]
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[[Category: Filament]]
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[[Category: Nucleotide metabolism]]
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[[Category: Oxidoreductase]]
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[[Category: Protein fibril]]
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[[Category: Ribonucleotide reductase]]
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Current revision

EM structure of Bacillus subtilis ribonucleotide reductase inhibited double-helical filament of NrdE alpha subunit with dATP

6myx, resolution 6.00Å

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