4bmo: Difference between revisions
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==Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)== | ==Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)== | ||
<StructureSection load='4bmo' size='340' side='right' caption='[[4bmo]], [[Resolution|resolution]] 1.81Å' scene=''> | <StructureSection load='4bmo' size='340' side='right'caption='[[4bmo]], [[Resolution|resolution]] 1.81Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4bmo]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4bmo]] 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=4BMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BMO FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></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=4bmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bmo OCA], [https://pdbe.org/4bmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bmo RCSB], [https://www.ebi.ac.uk/pdbsum/4bmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bmo ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [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 18: | Line 18: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4bmo" style="background-color:#fffaf0;"></div> | |||
==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: | [[Category: Bacillus cereus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Andersson | [[Category: Andersson KK]] | ||
[[Category: Hammerstad | [[Category: Hammerstad M]] | ||
[[Category: Hersleth | [[Category: Hersleth H-P]] | ||
[[Category: Rohr | [[Category: Rohr AK]] | ||
Latest revision as of 14:54, 20 December 2023
Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)
Structural highlights
FunctionQ81G55_BACCR Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).[PIRNR:PIRNR000355] Publication Abstract from PubMedClass 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 AlsoReferences
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