6tqz: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Crystal structure of ribonucleotide reductase NrdF L61G variant from Bacillus anthracis aerobically soaked with Fe(II) and Mn(II) ions==
-<StructureSection load='6tqz' size='340' side='right'caption='[[6tqz]]' scene=''>
+<StructureSection load='6tqz' size='340' side='right'caption='[[6tqz]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TQZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6tqz]] 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=6TQZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TQZ 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=6tqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqz OCA], [http://pdbe.org/6tqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqz RCSB], [http://www.ebi.ac.uk/pdbsum/6tqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqz 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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <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]], [[6tqx|6tqx]], [[6tqy|6tqy]]</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=6tqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tqz OCA], [http://pdbe.org/6tqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tqz RCSB], [http://www.ebi.ac.uk/pdbsum/6tqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tqz ProSAT]</span></td></tr>
 </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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6tqz" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[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]]