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| | <StructureSection load='6qo8' size='340' side='right'caption='[[6qo8]], [[Resolution|resolution]] 1.32Å' scene=''> | | <StructureSection load='6qo8' size='340' side='right'caption='[[6qo8]], [[Resolution|resolution]] 1.32Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6qo8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_sterne) Bacillus anthracis (strain sterne)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QO8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QO8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6qo8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._Sterne Bacillus anthracis str. Sterne]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QO8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.3192177Å</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=260799 Bacillus anthracis (strain Sterne)])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6qo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qo8 OCA], [https://pdbe.org/6qo8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qo8 RCSB], [https://www.ebi.ac.uk/pdbsum/6qo8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qo8 ProSAT]</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=6qo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qo8 OCA], [http://pdbe.org/6qo8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qo8 RCSB], [http://www.ebi.ac.uk/pdbsum/6qo8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qo8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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] | + | [https://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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6qo8" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6qo8" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Bacillus anthracis str. Sterne]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribonucleoside-diphosphate reductase]]
| + | [[Category: Grave K]] |
| - | [[Category: Grave, K]] | + | [[Category: Hogbom M]] |
| - | [[Category: Hogbom, M]] | + | |
| - | [[Category: 2'-deoxyribonucleotide metabolism]]
| + | |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Metal binding]]
| + | |
| - | [[Category: Oxidation reduction process]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| 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 PubMed
Class Ib ribonucleotide reductases (RNR) utilize a di-nuclear manganese or iron cofactor for reduction of superoxide or molecular oxygen, respectively. This generates a stable tyrosyl radical (Y.) in the R2 subunit (NrdF), which is further used for ribonucleotide reduction in the R1 subunit of RNR. Here, we report high-resolution crystal structures of Bacillus anthracis NrdF in the metal-free form (1.51 A) and in complex with manganese (Mn(II)/Mn(II), 1.30 A). We also report three structures of the protein in complex with iron, either prepared anaerobically (Fe(II)/Fe(II) form, 1.32 A), or prepared aerobically in the photo-reduced Fe(II)/Fe(II) form (1.63 A) and with the partially oxidized metallo-cofactor (1.46 A). The structures reveal significant conformational dynamics, likely to be associated with the generation, stabilization, and transfer of the radical to the R1 subunit. Based on observed redox-dependent structural changes, we propose that the passage for the superoxide, linking the FMN cofactor of NrdI and the metal site in NrdF, is closed upon metal oxidation, blocking access to the metal and radical sites. In addition, we describe the structural mechanics likely to be involved in this process.
Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access.,Grave K, Lambert W, Berggren G, Griese JJ, Bennett MD, Logan DT, Hogbom M J Biol Inorg Chem. 2019 Aug 13. pii: 10.1007/s00775-019-01703-z. doi:, 10.1007/s00775-019-01703-z. PMID:31410573[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Grave K, Lambert W, Berggren G, Griese JJ, Bennett MD, Logan DT, Hogbom M. Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access. J Biol Inorg Chem. 2019 Aug 13. pii: 10.1007/s00775-019-01703-z. doi:, 10.1007/s00775-019-01703-z. PMID:31410573 doi:http://dx.doi.org/10.1007/s00775-019-01703-z
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