1jpr: Difference between revisions

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[[Image:1jpr.jpg|left|200px]]


<!--
==Mn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxide==
The line below this paragraph, containing "STRUCTURE_1jpr", creates the "Structure Box" on the page.
<StructureSection load='1jpr' size='340' side='right'caption='[[1jpr]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1jpr]] 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=1JPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JPR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.88&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
{{STRUCTURE_1jpr| PDB=1jpr |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpr OCA], [https://pdbe.org/1jpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jpr RCSB], [https://www.ebi.ac.uk/pdbsum/1jpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jpr 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/jp/1jpr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1jpr ConSurf].
<div style="clear:both"></div>


'''Mn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxide'''
==See Also==
 
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The di-iron carboxylate proteins constitute a diverse class of non-heme iron enzymes performing a multitude of redox reactions. These reactions usually involve high-valent Fe-oxo species and are thought to be controlled by carboxylate shifts. Owing to their short lifetime, the intermediate structures have so far escaped structural characterization by X-ray crystallography. In an attempt to map the carboxylate conformations available to the protein during different redox states and different ligand environments, we have studied metal-substituted forms of the R2 protein of ribonucleotide reductase from Escherichia coli. In the present work we have solved the crystal structures of Mn-substituted R2 oxidized in two different ways. Oxidation was performed using either nitric oxide or a combination of hydrogen peroxide and hydroxylamine. The two structures are virtually identical, indicating that the oxidation states are the same, most likely a mixed-valent MnII-MnIII centre. One of the carboxylate ligands (D84) adopts a new, so far unseen, conformation, which could participate in the mechanism for radical generation in R2. E238 adopts a bridging-chelating conformation proposed to be important for proper O2 activation but not previously observed in the wild-type enzyme. Probable catalase activity was also observed during the oxidation with H2O2, indicating mechanistic similarities to the di-Mn catalases.
 
==About this Structure==
1JPR 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=1JPR OCA].
 
==Reference==
Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation., Hogbom M, Andersson ME, Nordlund P, J Biol Inorg Chem. 2001 Mar;6(3):315-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11315567 11315567]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Ribonucleoside-diphosphate reductase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Andersson ME]]
[[Category: Andersson, M E.]]
[[Category: Hogbom M]]
[[Category: Hogbom, M.]]
[[Category: Nordlund P]]
[[Category: Nordlund, P.]]
[[Category: Mn substituted]]
[[Category: Oxidized by no]]
[[Category: Radical protein]]
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Retrieved from "https://proteopedia.org/1jpr"