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[[Image:6r1r.gif|left|200px]]


{{Structure
==RIBONUCLEOTIDE REDUCTASE E441D MUTANT R1 PROTEIN FROM ESCHERICHIA COLI==
|PDB= 6r1r |SIZE=350|CAPTION= <scene name='initialview01'>6r1r</scene>, resolution 3.1&Aring;
<StructureSection load='6r1r' size='340' side='right'caption='[[6r1r]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
|SITE= <scene name='pdbsite=ACA:Active+Site+w.+Glutamate+441+Mutated+To+Aspartate'>ACA</scene>, <scene name='pdbsite=ACB:Active+Site+w.+Glutamate+441+Mutated+To+Aspartate'>ACB</scene> and <scene name='pdbsite=ACC:Active+Site+w.+Glutamate+441+Mutated+To+Aspartate'>ACC</scene>
== Structural highlights ==
|LIGAND=
<table><tr><td colspan='2'>[[6r1r]] is a 7 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=6R1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R1R 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]] 3.1&#8491;</td></tr>
|GENE= NRDA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6r1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1r OCA], [https://pdbe.org/6r1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r1r RCSB], [https://www.ebi.ac.uk/pdbsum/6r1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r1r ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
== Evolutionary Conservation ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6r1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1r OCA], [http://www.ebi.ac.uk/pdbsum/6r1r PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=6r1r RCSB]</span>
[[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/r1/6r1r_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=6r1r ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The invariant active site residue Glu441 in protein R1 of ribonucleotide reductase from Escherichia coli has been engineered to alanine, aspartic acid, and glutamic acid. Each mutant protein was structurally and enzymatically characterized. Glu441 contributes to substrate binding, and a carboxylate side chain at position 441 is essential for catalysis. The most intriguing results are the suicidal mechanism-based reaction intermediates observed when R1 E441Q is incubated with protein R2 and natural substrates (CDP and GDP). In a consecutive reaction sequence, we observe at least three clearly discernible steps: (i) a rapid decay (k1 &gt;/= 1.2 s-1) of the catalytically essential tyrosyl radical of protein R2 concomitant with formation of an early transient radical intermediate species, (ii) a slower decay (k2 = 0.03 s-1) of the early intermediate concomitant with formation of another intermediate with a triplet EPR signal, and (iii) decay (k3 = 0.004 s-1) of the latter concomitant with formation of a characteristic substrate degradation product. The characteristics of the triplet EPR signal are compatible with a substrate radical intermediate (most likely localized at the 3'-position of the ribose moiety of the substrate nucleotide) postulated to occur in the wild type reaction mechanism as well.


'''RIBONUCLEOTIDE REDUCTASE E441D MUTANT R1 PROTEIN FROM ESCHERICHIA COLI'''
A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase.,Persson AL, Eriksson M, Katterle B, Potsch S, Sahlin M, Sjoberg BM J Biol Chem. 1997 Dec 12;272(50):31533-41. PMID:9395490<ref>PMID:9395490</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6r1r" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The invariant active site residue Glu441 in protein R1 of ribonucleotide reductase from Escherichia coli has been engineered to alanine, aspartic acid, and glutamic acid. Each mutant protein was structurally and enzymatically characterized. Glu441 contributes to substrate binding, and a carboxylate side chain at position 441 is essential for catalysis. The most intriguing results are the suicidal mechanism-based reaction intermediates observed when R1 E441Q is incubated with protein R2 and natural substrates (CDP and GDP). In a consecutive reaction sequence, we observe at least three clearly discernible steps: (i) a rapid decay (k1 &gt;/= 1.2 s-1) of the catalytically essential tyrosyl radical of protein R2 concomitant with formation of an early transient radical intermediate species, (ii) a slower decay (k2 = 0.03 s-1) of the early intermediate concomitant with formation of another intermediate with a triplet EPR signal, and (iii) decay (k3 = 0.004 s-1) of the latter concomitant with formation of a characteristic substrate degradation product. The characteristics of the triplet EPR signal are compatible with a substrate radical intermediate (most likely localized at the 3'-position of the ribose moiety of the substrate nucleotide) postulated to occur in the wild type reaction mechanism as well.
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 
== References ==
==About this Structure==
<references/>
6R1R is a [[Protein complex]] structure of sequences 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=6R1R OCA].
__TOC__
 
</StructureSection>
==Reference==
A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase., Persson AL, Eriksson M, Katterle B, Potsch S, Sahlin M, Sjoberg BM, J Biol Chem. 1997 Dec 12;272(50):31533-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9395490 9395490]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Ribonucleoside-diphosphate reductase]]
[[Category: Eklund H]]
[[Category: Eklund, H.]]
[[Category: Eriksson M]]
[[Category: Eriksson, M.]]
[[Category: allosteric regulation]]
[[Category: complex (oxidoreductase/peptide)]]
[[Category: deoxyribonucleotide synthesis]]
[[Category: radical chemistry]]
[[Category: ribonucleotide reductase]]
[[Category: specificity]]
 
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