3mjo

From Proteopedia

(Difference between revisions)

Current revision

Small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes

Structural highlights

3mjo is a 2 chain structure with sequence from Corynebacterium ammoniagenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.36Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O69274_CORAM Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355]

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 X-ray crystallographic structure of the native R2F subunit of the ribonucleotide reductase (RNR) of Corynebacterium ammoniagenes ATCC 6872 is reported, with a resolution of 1.36 A. The metal site contains an oxo/hydroxo-bridged manganese dimer, located near a tyrosine residue (Y115). The coordination of the manganese dimer and its distance to a nearby tyrosine residue resemble the di-iron metalloradical cofactor of class I RNR from Escherichia coli . Multifrequency EPR measurements of the highly active C. ammoniagenes R2F subunit show that the metal site contains a ferromagnetically exchange-coupled Mn(III)Mn(III) dimer weakly coupled to a tyrosyl radical. A mechanism for the metalloradical cofactor (Mn(III)Mn(III)Y(*)) generation is proposed. H(2)O(2) (HO(2)(-)) instead of O(2) is hypothesized as physiological oxidant for the Mn dimer which in turn oxidizes the tyrosine Y115. Changes in the ligand sphere of both manganese ions during metalloradical generation direct the complex formation of this cofactor, disfavoring alternate reaction pathways such as H(2)O(2) dismutation, as observed for manganese catalase, a structural analogue of the R2F metal site. The presented results demonstrate the importance of manganese for radical formation in this RNR and confirm the assignment of this enzyme to class Ib.

A tyrosyl-dimanganese coupled spin system is the native metalloradical cofactor of the R2F subunit of the ribonucleotide reductase of Corynebacterium ammoniagenes.,Cox N, Ogata H, Stolle P, Reijerse E, Auling G, Lubitz W J Am Chem Soc. 2010 Aug 18;132(32):11197-213. PMID:20698687^[1]

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

References

↑ Cox N, Ogata H, Stolle P, Reijerse E, Auling G, Lubitz W. A tyrosyl-dimanganese coupled spin system is the native metalloradical cofactor of the R2F subunit of the ribonucleotide reductase of Corynebacterium ammoniagenes. J Am Chem Soc. 2010 Aug 18;132(32):11197-213. PMID:20698687 doi:10.1021/ja1036995

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/3mjo"

@@ Line 1: / Line 1: @@
 ==Small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes==
-<StructureSection load='3mjo' size='340' side='right' caption='[[3mjo]], [[Resolution|resolution]] 1.36&Aring;' scene=''>
+<StructureSection load='3mjo' size='340' side='right'caption='[[3mjo]], [[Resolution|resolution]] 1.36&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3mjo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_ammoniagenes"_cooke_and_keith_1927 "bacterium ammoniagenes" cooke and keith 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MJO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MJO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3mjo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_ammoniagenes Corynebacterium ammoniagenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MJO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MJO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</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]] 1.36&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrdF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1697 "Bacterium ammoniagenes" Cooke and Keith 1927])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene></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=3mjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mjo OCA], [http://pdbe.org/3mjo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mjo RCSB], [http://www.ebi.ac.uk/pdbsum/3mjo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mjo ProSAT]</span></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=3mjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mjo OCA], [https://pdbe.org/3mjo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mjo RCSB], [https://www.ebi.ac.uk/pdbsum/3mjo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mjo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/O69274_CORAM O69274_CORAM]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355]
+[https://www.uniprot.org/uniprot/O69274_CORAM O69274_CORAM] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355]
 == 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/mj/3mjo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mj/3mjo_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 3mjo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacterium ammoniagenes cooke and keith 1927]]
+[[Category: Corynebacterium ammoniagenes]]
-[[Category: Auling, G]]
+[[Category: Large Structures]]
-[[Category: Lubitz, W]]
+[[Category: Auling G]]
-[[Category: Ogata, H]]
+[[Category: Lubitz W]]
-[[Category: Stehr, M]]
+[[Category: Ogata H]]
-[[Category: Stolle, P]]
+[[Category: Stehr M]]
-[[Category: Dna-precursor biosynthesis]]
+[[Category: Stolle P]]
-[[Category: Metallocofactor]]
-[[Category: Mn ribonucleotide reductase]]
-[[Category: Oxidoreductase]]
-[[Category: Radical enzyme]]
-[[Category: Rnr]]
-[[Category: Split signal]]

3mjo

From Proteopedia

Current revision

Small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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