2xof: Difference between revisions
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==Ribonucleotide reductase Y122NO2Y modified R2 subunit of E. coli== | |||
<StructureSection load='2xof' size='340' side='right'caption='[[2xof]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2xof]] is a 2 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=2XOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XOF 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]] 2.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</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=2xof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xof OCA], [https://pdbe.org/2xof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xof RCSB], [https://www.ebi.ac.uk/pdbsum/2xof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xof 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. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xo/2xof_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2xof ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Escherichia coli ribonucleotide reductase is an alpha2beta2 complex that catalyzes the conversion of nucleotides to deoxynucleotides and requires a diferric-tyrosyl radical (Y(*)) cofactor to initiate catalysis. The initiation process requires long-range proton-coupled electron transfer (PCET) over 35 A between the two subunits by a specific pathway (Y(122)(*)-->W(48)-->Y(356) within beta to Y(731)-->Y(730)-->C(439) within alpha). The rate-limiting step in nucleotide reduction is the conformational gating of the PCET process, which masks the chemistry of radical propagation. 3-Nitrotyrosine (NO(2)Y) has recently been incorporated site-specifically in place of Y(122) in beta2. The protein as isolated contained a diferric cluster but no nitrotyrosyl radical (NO(2)Y(*)) and was inactive. In the present paper we show that incubation of apo-Y(122)NO(2)Y-beta2 with Fe(2+) and O(2) generates a diferric-NO(2)Y(*) that has a half-life of 40 s at 25 degrees C. Sequential mixing experiments, in which the cofactor is assembled to 1.2 NO(2)Y(*)/beta2 and then mixed with alpha2, CDP, and ATP, have been analyzed by stopped-flow absorption spectroscopy, rapid freeze quench EPR spectroscopy, and rapid chemical quench methods. These studies have, for the first time, unmasked the conformational gating. They reveal that the NO(2)Y(*) is reduced to the nitrotyrosinate with biphasic kinetics (283 and 67 s(-1)), that dCDP is produced at 107 s(-1), and that a new Y(*) is produced at 97 s(-1). Studies with pathway mutants suggest that the new Y(*) is predominantly located at 356 in beta2. In consideration of these data and the crystal structure of Y(122)NO(2)Y-beta2, a mechanism for PCET uncoupling in NO(2)Y(*)-RNR is proposed. | |||
A Hot Oxidant, 3-NO(2)Y(122) Radical, Unmasks Conformational Gating in Ribonucleotide Reductase.,Yokoyama K, Uhlin U, Stubbe J J Am Chem Soc. 2010 Oct 7. PMID:20929229<ref>PMID:20929229</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2xof" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] | |||
*[[Ribonucleotide reductase|Ribonucleotide reductase]] | == References == | ||
<references/> | |||
== | __TOC__ | ||
< | </StructureSection> | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli K-12]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Stubbe | [[Category: Stubbe J]] | ||
[[Category: Uhlin | [[Category: Uhlin U]] | ||
[[Category: Yokoyama | [[Category: Yokoyama K]] | ||
