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==Crystal structure of apo (metal-free) ribonucleotide reductase NrdF L61G variant from Bacillus anthracis== | ==Crystal structure of apo (metal-free) ribonucleotide reductase NrdF L61G variant from Bacillus anthracis== | ||
<StructureSection load='6tqx' size='340' side='right'caption='[[6tqx]]' scene=''> | <StructureSection load='6tqx' size='340' side='right'caption='[[6tqx]], [[Resolution|resolution]] 2.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQX FirstGlance]. <br> | <table><tr><td colspan='2'>[[6tqx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQX FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqx OCA], [http://pdbe.org/6tqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqx RCSB], [http://www.ebi.ac.uk/pdbsum/6tqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqx ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6tqv|6tqv]], [[6tqw|6tqw]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrdF, GBAA_1372 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</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://proteopedia.org/fgij/fg.htm?mol=6tqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqx OCA], [http://pdbe.org/6tqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqx RCSB], [http://www.ebi.ac.uk/pdbsum/6tqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqx ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/Q81TB4_BACAN Q81TB4_BACAN]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving-Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4-carboxylate 2-histidine coordination sphere, are known to require either a Fe/Fe, Mn/Fe or Mn/Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn/Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn/Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal-free protein is subjected to incubation with Mn(II) and Fe(II) in equal concentrations. This observation provides an example of a protein scaffold intrinsically predisposed to defy the Irving-Williams series and supports the assumption that the Mn/Mn cofactor is the biologically relevant cofactor in vivo. Substitution of a second coordination sphere residue changes the spontaneous metallation of the protein to predominantly form a heterodinuclear Mn/Fe cofactor under aerobic conditions and a Mn/Mn metal center under anoxic conditions. Together, the results describe the intrinsic metal specificity of class Ib RNR and provide insight into control mechanisms for protein metallation. | |||
The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.,Grave K, Griese JJ, Berggren G, Bennett MD, Hogbom M J Biol Inorg Chem. 2020 Apr 15. pii: 10.1007/s00775-020-01782-3. doi:, 10.1007/s00775-020-01782-3. PMID:32296998<ref>PMID:32296998</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6tqx" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Grave K]] | [[Category: Ribonucleoside-diphosphate reductase]] | ||
[[Category: Hogbom M]] | [[Category: Grave, K]] | ||
[[Category: Hogbom, M]] | |||
[[Category: 2'-deoxyribonucleotide metabolism]] | |||
[[Category: Dna replication]] | |||
[[Category: Metal binding]] | |||
[[Category: Oxidation reduction process]] | |||
[[Category: Oxidoreductase]] | |||
Revision as of 10:11, 29 April 2020
Crystal structure of apo (metal-free) ribonucleotide reductase NrdF L61G variant from Bacillus anthracisCrystal structure of apo (metal-free) ribonucleotide reductase NrdF L61G variant from Bacillus anthracis
Structural highlights
Function[Q81TB4_BACAN] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355] Publication Abstract from PubMedCorrect protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving-Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4-carboxylate 2-histidine coordination sphere, are known to require either a Fe/Fe, Mn/Fe or Mn/Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn/Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn/Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal-free protein is subjected to incubation with Mn(II) and Fe(II) in equal concentrations. This observation provides an example of a protein scaffold intrinsically predisposed to defy the Irving-Williams series and supports the assumption that the Mn/Mn cofactor is the biologically relevant cofactor in vivo. Substitution of a second coordination sphere residue changes the spontaneous metallation of the protein to predominantly form a heterodinuclear Mn/Fe cofactor under aerobic conditions and a Mn/Mn metal center under anoxic conditions. Together, the results describe the intrinsic metal specificity of class Ib RNR and provide insight into control mechanisms for protein metallation. The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.,Grave K, Griese JJ, Berggren G, Bennett MD, Hogbom M J Biol Inorg Chem. 2020 Apr 15. pii: 10.1007/s00775-020-01782-3. doi:, 10.1007/s00775-020-01782-3. PMID:32296998[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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