|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal Structure of Ribonucleotide Reductase apo-NrdF from Bacillus cereus (space group P21)== | | ==Crystal Structure of Ribonucleotide Reductase apo-NrdF from Bacillus cereus (space group P21)== |
| - | <StructureSection load='4bmr' size='340' side='right' caption='[[4bmr]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='4bmr' size='340' side='right'caption='[[4bmr]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4bmr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BMR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4bmr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BMR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4bmo|4bmo]], [[4bmp|4bmp]], [[4bmq|4bmq]], [[4bmt|4bmt]]</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></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=4bmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bmr OCA], [https://pdbe.org/4bmr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bmr RCSB], [https://www.ebi.ac.uk/pdbsum/4bmr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bmr 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=4bmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bmr OCA], [http://pdbe.org/4bmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bmr RCSB], [http://www.ebi.ac.uk/pdbsum/4bmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bmr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q81G55_BACCR Q81G55_BACCR]] 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/Q81G55_BACCR Q81G55_BACCR] 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 == |
| Line 22: |
Line 21: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Ribonucleotide reductase|Ribonucleotide reductase]] | + | *[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 14579]] | + | [[Category: Bacillus cereus]] |
| - | [[Category: Ribonucleoside-diphosphate reductase]] | + | [[Category: Large Structures]] |
| - | [[Category: Andersson, K K]] | + | [[Category: Andersson KK]] |
| - | [[Category: Hammerstad, M]] | + | [[Category: Hammerstad M]] |
| - | [[Category: Hersleth, H P]] | + | [[Category: Hersleth H-P]] |
| - | [[Category: Rohr, A K]] | + | [[Category: Rohr AK]] |
| - | [[Category: Tomter, A B]] | + | [[Category: Tomter AB]] |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
Q81G55_BACCR Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355]
Publication Abstract from PubMed
Class Ib ribonucleotide reductases (RNRs) use a dimetal-tyrosyl radical (Y*) cofactor in their NrdF (beta2) subunit to initiate ribonucleotide reduction in the NrdE (alpha2) subunit. Contrary to the diferric tyrosyl radical (Fe(III)2-Y*) cofactor, which can self-assemble from Fe(II)2-NrdF and O2, generation of the Mn(III)2-Y* cofactor requires the reduced form of a flavoprotein, NrdIhq, and O2 for its assembly. Here we report the 1.8 A resolution crystal structure of Bacillus cereus Fe2-NrdF in complex with NrdI. Compared to the previously solved Escherichia coli NrdI-Mn(II)2-NrdF structure, NrdI and NrdF binds similarly in Bacillus cereus through conserved core interactions. This protein-protein association seems to be unaffected by metal ion type bound in the NrdF subunit. The Bacillus cereus Mn(II)2-NrdF and Fe2-NrdF structures, also presented here, show conformational flexibility of residues surrounding the NrdF metal ion site. The movement of one of the metal-coordinating carboxylates is linked to the metal type present at the dimetal site and not associated with NrdI-NrdF binding. This carboxylate conformation seems to be vital for the water network connecting the NrdF dimetal site and the flavin in NrdI. From these observations, we suggest that metal-dependent variations in carboxylate coordination geometries are important for active Y* cofactor generation in class Ib RNRs. Additionally, we show that binding of NrdI to NrdF would structurally interfere with the suggested alpha2beta2 (NrdE-NrdF) holoenzyme formation, suggesting the potential requirement for NrdI dissociation before NrdE-NrdF assembly after NrdI-activation. The mode of interactions between the proteins involved in the class Ib RNR system is, however, not fully resolved.
Crystal Structure of Bacillus cereus Class Ib Ribonucleotide Reductase Di-iron NrdF in Complex with NrdI.,Hammerstad M, Hersleth HP, Tomter AB, Rohr AK, Andersson KK ACS Chem Biol. 2014 Feb 21;9(2):526-37. doi: 10.1021/cb400757h. Epub 2013 Dec 11. PMID:24295378[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hammerstad M, Hersleth HP, Tomter AB, Rohr AK, Andersson KK. Crystal Structure of Bacillus cereus Class Ib Ribonucleotide Reductase Di-iron NrdF in Complex with NrdI. ACS Chem Biol. 2014 Feb 21;9(2):526-37. doi: 10.1021/cb400757h. Epub 2013 Dec 11. PMID:24295378 doi:http://dx.doi.org/10.1021/cb400757h
|
