5ci2: Difference between revisions
New page: '''Unreleased structure''' The entry 5ci2 is ON HOLD Authors: Funk, M.A., Drennan, C.L. Description: Ribonucleotide reductase Y122 2,3,6-F3Y variant Category: Unreleased Structures... |
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The | ==Ribonucleotide reductase Y122 2,3,6-F3Y variant== | ||
<StructureSection load='5ci2' size='340' side='right'caption='[[5ci2]], [[Resolution|resolution]] 2.25Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ci2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CI2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CI2 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]] 2.25Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=51T:2,3,6-TRIFLUORO-L-TYROSINE'>51T</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ci2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ci2 OCA], [https://pdbe.org/5ci2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ci2 RCSB], [https://www.ebi.ac.uk/pdbsum/5ci2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ci2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://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. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Fluorinated tyrosines (FnY's, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y's, a stable Y radical (Y.) in the beta subunit (position 122 in E. coli), and three transiently oxidized Y's (356 in beta and 731 and 730 in alpha) to initiate the radical-dependent nucleotide reduction process. FnY (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-beta and the X-ray structures of each resulting beta with a diferric cluster are reported and compared with wt-beta2 crystallized under the same conditions. The essential diferric-FnY. cofactor is self-assembled from apo FnY-beta2, Fe2+, and O2 to produce approximately 1 Y./beta2 and approximately 3 Fe3+/beta2. The FnY. are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-beta2. Each FnY.-beta2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field electron nuclear double resonance spectroscopies. The hyperfine interactions associated with the 19F nucleus provide unique signatures of each FnY. that are readily distinguishable from unlabeled Y.'s. The variability of the abiotic FnY pKa's (6.4 to 7.8) and reduction potentials (-30 to +130 mV relative to Y at pH 7.5) provide probes of enzymatic reactions proposed to involve Y.'s in catalysis and to investigate the importance and identity of hopping Y.'s within redox active proteins proposed to protect them from uncoupled radical chemistry. | |||
Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example.,Oyala PH, Ravichandran KR, Funk MA, Stucky PA, Stich TA, Drennan CL, Britt RD, Stubbe J J Am Chem Soc. 2016 Jun 21. PMID:27276098<ref>PMID:27276098</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5ci2" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
==See Also== | |||
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli O157:H7]] | |||
[[Category: Large Structures]] | |||
[[Category: Drennan CL]] | |||
[[Category: Funk MA]] | |||
Latest revision as of 11:38, 27 September 2023
Ribonucleotide reductase Y122 2,3,6-F3Y variantRibonucleotide reductase Y122 2,3,6-F3Y variant
Structural highlights
FunctionRIR2_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. Publication Abstract from PubMedFluorinated tyrosines (FnY's, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y's, a stable Y radical (Y.) in the beta subunit (position 122 in E. coli), and three transiently oxidized Y's (356 in beta and 731 and 730 in alpha) to initiate the radical-dependent nucleotide reduction process. FnY (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-beta and the X-ray structures of each resulting beta with a diferric cluster are reported and compared with wt-beta2 crystallized under the same conditions. The essential diferric-FnY. cofactor is self-assembled from apo FnY-beta2, Fe2+, and O2 to produce approximately 1 Y./beta2 and approximately 3 Fe3+/beta2. The FnY. are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-beta2. Each FnY.-beta2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field electron nuclear double resonance spectroscopies. The hyperfine interactions associated with the 19F nucleus provide unique signatures of each FnY. that are readily distinguishable from unlabeled Y.'s. The variability of the abiotic FnY pKa's (6.4 to 7.8) and reduction potentials (-30 to +130 mV relative to Y at pH 7.5) provide probes of enzymatic reactions proposed to involve Y.'s in catalysis and to investigate the importance and identity of hopping Y.'s within redox active proteins proposed to protect them from uncoupled radical chemistry. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example.,Oyala PH, Ravichandran KR, Funk MA, Stucky PA, Stich TA, Drennan CL, Britt RD, Stubbe J J Am Chem Soc. 2016 Jun 21. PMID:27276098[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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