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[[Image:1yfd.gif|left|200px]]


{{Structure
==Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli==
|PDB= 1yfd |SIZE=350|CAPTION= <scene name='initialview01'>1yfd</scene>, resolution 1.90&Aring;
<StructureSection load='1yfd' size='340' side='right'caption='[[1yfd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND= <scene name='pdbligand=F2O:MU-OXO-DIIRON(III)'>F2O</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>
<table><tr><td colspan='2'>[[1yfd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YFD FirstGlance]. <br>
|ACTIVITY= <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><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
|GENE= nrdB, ftsB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<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=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfd OCA], [https://pdbe.org/1yfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yfd RCSB], [https://www.ebi.ac.uk/pdbsum/1yfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yfd ProSAT]</span></td></tr>
|RELATEDENTRY=[[1biq|1BIQ]], [[1pfr|1PFR]], [[1xik|1XIK]], [[1mxr|1MXR]], [[1pim|1PIM]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfd OCA], [http://www.ebi.ac.uk/pdbsum/1yfd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yfd RCSB]</span>
== 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/yf/1yfd_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=1yfd ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.


'''Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli'''
A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies.,Kolberg M, Logan DT, Bleifuss G, Potsch S, Sjoberg BM, Graslund A, Lubitz W, Lassmann G, Lendzian F J Biol Chem. 2005 Mar 25;280(12):11233-46. Epub 2005 Jan 5. PMID:15634667<ref>PMID:15634667</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1yfd" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1YFD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFD OCA].
__TOC__
 
</StructureSection>
==Reference==
A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies., Kolberg M, Logan DT, Bleifuss G, Potsch S, Sjoberg BM, Graslund A, Lubitz W, Lassmann G, Lendzian F, J Biol Chem. 2005 Mar 25;280(12):11233-46. Epub 2005 Jan 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15634667 15634667]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Ribonucleoside-diphosphate reductase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Bleifuss G]]
[[Category: Bleifuss, G.]]
[[Category: Graeslund A]]
[[Category: Graeslund, A.]]
[[Category: Kolberg M]]
[[Category: Kolberg, M.]]
[[Category: Lassmann G]]
[[Category: Lassmann, G.]]
[[Category: Lendzian F]]
[[Category: Lendzian, F.]]
[[Category: Logan DT]]
[[Category: Logan, D T.]]
[[Category: Lubitz W]]
[[Category: Lubitz, W.]]
[[Category: Poetsch S]]
[[Category: Poetsch, S.]]
[[Category: Sjoeberg BM]]
[[Category: Sjoeberg, B M.]]
[[Category: di-iron center]]
 
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Retrieved from "https://proteopedia.org/1yfd"