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


{{Structure
==Mn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxide==
|PDB= 1jpr |SIZE=350|CAPTION= <scene name='initialview01'>1jpr</scene>, resolution 1.88&Aring;
<StructureSection load='1jpr' size='340' side='right'caption='[[1jpr]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=HG:MERCURY (II) ION'>HG</scene>
<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>
|ACTIVITY= [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]  
</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>
|GENE=  
<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>
}}
<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: HG]]
[[Category: MN]]
[[Category: mn substituted]]
[[Category: oxidized by no]]
[[Category: radical protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:06:43 2008''

Latest revision as of 16:24, 13 March 2024

Mn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxideMn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxide

Structural highlights

1jpr is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.88Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1jpr, resolution 1.88Å

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