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| | ==X-ray crystal structure of Streptococcus sanguinis dimanganese(II)-NrdF== | | ==X-ray crystal structure of Streptococcus sanguinis dimanganese(II)-NrdF== |
| - | <StructureSection load='4n83' size='340' side='right' caption='[[4n83]], [[Resolution|resolution]] 2.65Å' scene=''> | + | <StructureSection load='4n83' size='340' side='right'caption='[[4n83]], [[Resolution|resolution]] 2.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4n83]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsv Strsv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N83 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N83 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4n83]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_sanguinis_SK36 Streptococcus sanguinis SK36]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N83 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N83 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]] 2.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4n82|4n82]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrdF, SSA_0768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=388919 STRSV])</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=4n83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n83 OCA], [https://pdbe.org/4n83 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n83 RCSB], [https://www.ebi.ac.uk/pdbsum/4n83 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n83 ProSAT]</span></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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4n83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n83 OCA], [http://pdbe.org/4n83 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n83 RCSB], [http://www.ebi.ac.uk/pdbsum/4n83 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n83 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A3CLZ4_STRSV A3CLZ4_STRSV]] 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/A3CLZ4_STRSV A3CLZ4_STRSV] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[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 4n83" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4n83" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ribonucleoside-diphosphate reductase]] | + | [[Category: Large Structures]] |
| - | [[Category: Strsv]] | + | [[Category: Streptococcus sanguinis SK36]] |
| - | [[Category: Boal, A K]] | + | [[Category: Boal AK]] |
| - | [[Category: Rosenzweig, A C]] | + | [[Category: Rosenzweig AC]] |
| - | [[Category: Flavin mononucleotide]]
| + | |
| - | [[Category: Manganese]]
| + | |
| - | [[Category: Oxidation-reduction]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
A3CLZ4_STRSV Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355]
Publication Abstract from PubMed
Streptococcus sanguinis is a causative agent of infective endocarditis. Deletion of SsaB, a manganese transporter, drastically reduces S. sanguinis virulence. Many pathogenic organisms require class Ib RNR5 to catalyze the conversion of nucleotides to deoxynucleotides under aerobic conditions and recent studies demonstrate that this enzyme uses a dimanganese-tyrosyl radical (MnIII2-Y*) cofactor in vivo. The proteins required for S. sanguinis ribonucleotide reduction (NrdE and NrdF, alpha and beta subunits of RNR; NrdH and TrxR, a glutaredoxin-like thioredoxin and a thioredoxin reductase; and NrdI, a flavodoxin essential for assembly of RNRs metallo-cofactor) have been identified and characterized. Apo-NrdF with FeII and O2 can self-assemble a diferric-tyrosyl radical (FeIII2-Y*) cofactor (1.2 Y*/beta2) and with the help of NrdI, can assemble a MnIII2-Y* cofactor (0.9 Y*/beta2). The activity of RNR with its endogenous reductants, NrdH and TrxR, is 5,000 and 1,500 U/mg for the Mn- and Fe-NrdFs respectively. X-ray structures of S. sanguinis NrdIox and MnII2-NrdF are reported and provide a possible rationale for the weak affinity (2.9 muM) between them. These streptococcal proteins form a structurally distinct subclass relative to other Ib proteins with unique features likely important in cluster assembly including a long and negatively charged loop near the NrdI flavin and a bulky residue (Thr) at a constriction in the oxidant channel to the NrdI interface. These studies set the stage for identifying the active form of S. sanguinis class Ib RNR in an animal model for infective endocarditis and establishing whether the Mn requirement for pathogenesis is associated with RNR.
Streptococcus sanguinis Class Ib Ribonucleotide Reductase: High Activity with Both Iron and Manganese Cofactors and Structural Insights.,Makhlynets O, Boal AK, Rhodes DV, Kitten T, Rosenzweig AC, Stubbe J J Biol Chem. 2013 Dec 31. PMID:24381172[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Makhlynets O, Boal AK, Rhodes DV, Kitten T, Rosenzweig AC, Stubbe J. Streptococcus sanguinis Class Ib Ribonucleotide Reductase: High Activity with Both Iron and Manganese Cofactors and Structural Insights. J Biol Chem. 2013 Dec 31. PMID:24381172 doi:http://dx.doi.org/10.1074/jbc.M113.533554
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