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4erp

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==Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex==
==Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex==
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<StructureSection load='4erp' size='340' side='right' caption='[[4erp]], [[Resolution|resolution]] 4.45&Aring;' scene=''>
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<StructureSection load='4erp' size='340' side='right'caption='[[4erp]], [[Resolution|resolution]] 4.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4erp]] is a 8 chain structure with sequence from [http://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=4ERP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ERP FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4erp]] is a 8 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=4ERP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ERP FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</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">X-ray diffraction, [[Resolution|Resolution]] 4.45&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4erm|4erm]]</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), b2235, ftsB, JW2229, nrdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=4erp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4erp OCA], [https://pdbe.org/4erp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4erp RCSB], [https://www.ebi.ac.uk/pdbsum/4erp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4erp 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4erp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4erp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4erp RCSB], [http://www.ebi.ac.uk/pdbsum/4erp PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines. [[http://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.
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[https://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving formation of RNR subunits into alpha4beta4 rings. Here, we present the first X-ray structure of a gemcitabine-inhibited E. coli RNR and show that the previously described alpha4beta4 rings can interlock to form an unprecedented (alpha4beta4)2 megacomplex. This complex is also seen in a higher-resolution dATP-inhibited RNR structure presented here, which employs a distinct crystal lattice from that observed in the gemcitabine-inhibited case. With few reported examples of protein catenanes, we use data from small-angle X-ray scattering and electron microscopy to both understand the solution conditions that contribute to concatenation in RNRs as well as present a mechanism for the formation of these unusual structures.
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Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.,Zimanyi CM, Ando N, Brignole EJ, Asturias FJ, Stubbe J, Drennan CL Structure. 2012 Aug 8;20(8):1374-83. Epub 2012 Jun 21. PMID:22727814<ref>PMID:22727814</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>
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[[Category: Escherichia coli k-12]]
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[[Category: Escherichia coli K-12]]
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[[Category: Ribonucleoside-diphosphate reductase]]
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[[Category: Large Structures]]
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[[Category: Drennan, C L]]
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[[Category: Drennan CL]]
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[[Category: Zimanyi, C M]]
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[[Category: Zimanyi CM]]
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[[Category: Alpha/beta barrel]]
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[[Category: Atp cone]]
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[[Category: Cytosol]]
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[[Category: Diiron center]]
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[[Category: Oxidoreductase]]
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[[Category: Protein-protein complex]]
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[[Category: Ribonucleotide reduction]]
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[[Category: Rnr alpha]]
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[[Category: Rnr beta]]
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[[Category: Thioredoxin]]
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Current revision

Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex

PDB ID 4erp

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