3n3b

From Proteopedia

(Difference between revisions)

Current revision

Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide

Structural highlights

3n3b is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.36Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIR4_ECOLI Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F 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.

Publication Abstract from PubMed

The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)(2)-tyrosyl radical (Y*) or a Fe(III)(2)-Y* cofactor in the NrdF subunit. Whereas Fe(III)(2)-Y* can self-assemble from Fe(II)(2)-NrdF and O(2), activation of Mn(II)(2)-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O(2). The crystal structures reported here of E. coli Mn(II)(2)-NrdF and Fe(II)(2)-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)(2)-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)(2) active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)(2)-Y* cofactor assembly.

Structural Basis for Activation of Class Ib Ribonucleotide Reductase.,Boal AK, Cotruvo JA Jr, Stubbe J, Rosenzweig AC Science. 2010 Aug 5. PMID:20688982^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Boal AK, Cotruvo JA Jr, Stubbe J, Rosenzweig AC. Structural Basis for Activation of Class Ib Ribonucleotide Reductase. Science. 2010 Aug 5. PMID:20688982 doi:10.1126/science.1190187

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3n3b"

@@ Line 1: / Line 1: @@
 ==Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide==
-<StructureSection load='3n3b' size='340' side='right' caption='[[3n3b]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
+<StructureSection load='3n3b' size='340' side='right'caption='[[3n3b]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3n3b]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N3B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3n3b]] is a 4 chain structure with sequence from [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=3N3B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N3B FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.36&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3n37|3n37]], [[3n38|3n38]], [[3n39|3n39]], [[3n3a|3n3a]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2676, JW2651, nrdF, ygaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), nrdI, ygaO, b2674, JW2649 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3n3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n3b OCA], [https://pdbe.org/3n3b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n3b RCSB], [https://www.ebi.ac.uk/pdbsum/3n3b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n3b ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3n3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n3b OCA], [http://pdbe.org/3n3b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n3b RCSB], [http://www.ebi.ac.uk/pdbsum/3n3b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n3b ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RIR4_ECOLI RIR4_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F contains the tyrosyl radical required for catalysis. [[http://www.uniprot.org/uniprot/NRDI_ECOLI NRDI_ECOLI]] Probably involved in ribonucleotide reductase function.
+[https://www.uniprot.org/uniprot/RIR4_ECOLI RIR4_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F 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/n3/3n3b_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n3/3n3b_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 31: @@
 ==See Also==
-*[[Ribonucleotide reductase|Ribonucleotide reductase]]
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Ribonucleoside-diphosphate reductase]]
+[[Category: Large Structures]]
-[[Category: Boal, A K]]
+[[Category: Boal AK]]
-[[Category: Cotruvo, J A]]
+[[Category: Cotruvo Jr JA]]
-[[Category: Rosenzweig, A C]]
+[[Category: Rosenzweig AC]]
-[[Category: Stubbe, J]]
+[[Category: Stubbe J]]
-[[Category: Dimanganese cluster]]
-[[Category: Flavoprotein]]
-[[Category: Four-helix bundle]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxide]]
-[[Category: Ribonucleotide reductase]]

3n3b

From Proteopedia

Current revision

Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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