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==X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)==
==X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)==
<StructureSection load='6cwp' size='340' side='right' caption='[[6cwp]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
<StructureSection load='6cwp' size='340' side='right'caption='[[6cwp]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6cwp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Cytophaga_johnsonae Cytophaga johnsonae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CWP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CWP FirstGlance]. <br>
<table><tr><td colspan='2'>[[6cwp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_johnsoniae Flavobacterium johnsoniae] and [https://en.wikipedia.org/wiki/Flavobacterium_johnsoniae_UW101 Flavobacterium johnsoniae UW101]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CWP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CWP FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.92&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Fjoh_4066 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=376686 Cytophaga johnsonae])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6cwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cwp OCA], [http://pdbe.org/6cwp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cwp RCSB], [http://www.ebi.ac.uk/pdbsum/6cwp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cwp 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=6cwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cwp OCA], [https://pdbe.org/6cwp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cwp RCSB], [https://www.ebi.ac.uk/pdbsum/6cwp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cwp ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A5FCJ5_FLAJ1 A5FCJ5_FLAJ1]
A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its beta subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O2(-)) for activation, but it does not require the O2(-)-supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj beta has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj beta directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) betas. This tendency makes Fj beta unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O2(-) to the Mn2(II/II) cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj beta is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-beta.


Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor.,Rose HR, Ghosh MK, Maggiolo AO, Pollock CJ, Blaesi EJ, Hajj V, Wei Y, Rajakovich LJ, Chang WC, Han Y, Hajj M, Krebs C, Silakov A, Pandelia ME, Bollinger JM Jr., Boal AK Biochemistry. 2018 Apr 17. doi: 10.1021/acs.biochem.8b00247. PMID:29609464<ref>PMID:29609464</ref>
==See Also==
 
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6cwp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cytophaga johnsonae]]
[[Category: Flavobacterium johnsoniae]]
[[Category: Boal, A K]]
[[Category: Flavobacterium johnsoniae UW101]]
[[Category: Maggiolo, A O]]
[[Category: Large Structures]]
[[Category: Rose, H R]]
[[Category: Boal AK]]
[[Category: Dimanganese cluster]]
[[Category: Maggiolo AO]]
[[Category: Four-helix bundle]]
[[Category: Rose HR]]
[[Category: Oxidoreductase]]
[[Category: Oxidoretuctase]]
[[Category: Ribonucleotide reductase]]

Latest revision as of 17:31, 13 March 2024

X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)

Structural highlights

6cwp is a 3 chain structure with sequence from Flavobacterium johnsoniae and Flavobacterium johnsoniae UW101. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.92Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A5FCJ5_FLAJ1

See Also

6cwp, resolution 1.92Å

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