2xo5: Difference between revisions
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==RIBONUCLEOTIDE REDUCTASE Y731NH2Y MODIFIED R1 SUBUNIT OF E. COLI== | |||
<StructureSection load='2xo5' size='340' side='right'caption='[[2xo5]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2xo5]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [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=2XO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XO5 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]] 2.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TY2:3-AMINO-L-TYROSINE'>TY2</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=2xo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xo5 OCA], [https://pdbe.org/2xo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xo5 RCSB], [https://www.ebi.ac.uk/pdbsum/2xo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xo5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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. | |||
== 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/2xo5_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=2xo5 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Escherichia coli ribonucleotide reductase is an alpha2beta2 complex and catalyzes the conversion of nucleoside 5'-diphosphates (NDPs) to 2'-deoxynucleotides (dNDPs). The reaction is initiated by the transient oxidation of an active-site cysteine (C(439)) in alpha2 by a stable diferric tyrosyl radical (Y(122)*) cofactor in beta2. This oxidation occurs by a mechanism of long-range proton-coupled electron transfer (PCET) over 35 A through a specific pathway of residues: Y(122)*--> W(48)--> Y(356) in beta2 to Y(731)--> Y(730)--> C(439) in alpha2. To study the details of this process, 3-aminotyrosine (NH(2)Y) has been site-specifically incorporated in place of Y(356) of beta. The resulting protein, Y(356)NH(2)Y-beta2, and the previously generated proteins Y(731)NH(2)Y-alpha2 and Y(730)NH(2)Y-alpha2 (NH(2)Y-RNRs) are shown to catalyze dNDP production in the presence of the second subunit, substrate (S), and allosteric effector (E) with turnover numbers of 0.2-0.7 s(-1). Evidence acquired by three different methods indicates that the catalytic activity is inherent to NH(2)Y-RNRs and not the result of copurifying wt enzyme. The kinetics of formation of 3-aminotyrosyl radical (NH(2)Y*) at position 356, 731, and 730 have been measured with all S/E pairs. In all cases, NH(2)Y* formation is biphasic (k(fast) of 9-46 s(-1) and k(slow) of 1.5-5.0 s(-1)) and kinetically competent to be an intermediate in nucleotide reduction. The slow phase is proposed to report on the conformational gating of NH(2)Y* formation, while the k(cat) of approximately 0.5 s(-1) is proposed to be associated with rate-limiting oxidation by NH(2)Y* of the subsequent amino acid on the pathway during forward PCET. The X-ray crystal structures of Y(730)NH(2)Y-alpha2 and Y(731)NH(2)Y-alpha2 have been solved and indicate minimal structural changes relative to wt-alpha2. From the data, a kinetic model for PCET along the radical propagation pathway is proposed. | |||
Kinetics of Radical Intermediate Formation and Deoxynucleotide Production in 3-Aminotyrosine-Substituted Escherichia coli Ribonucleotide Reductases.,Minnihan EC, Seyedsayamdost MR, Uhlin U, Stubbe J J Am Chem Soc. 2011 Jun 22;133(24):9430-40. Epub 2011 May 25. PMID:21612216<ref>PMID:21612216</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2xo5" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Ribonucleotide reductase|Ribonucleotide reductase]] | *[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Minnihan EC]] | ||
[[Category: | [[Category: Seyedsayamdost MR]] | ||
[[Category: | [[Category: Stubbe J]] | ||
[[Category: | [[Category: Uhlin U]] | ||