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==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=''> | |||
== 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> | |||
</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> | |||
<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='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=4bmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bmr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bmr RCSB], [http://www.ebi.ac.uk/pdbsum/4bmr PDBsum]</span></td></tr> | |||
</table> | |||
== 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] | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:24295378</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== | ==See Also== | ||
*[[Ribonucleotide reductase|Ribonucleotide reductase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Atcc 14579]] | |||
[[Category: Ribonucleoside-diphosphate reductase]] | [[Category: Ribonucleoside-diphosphate reductase]] | ||
[[Category: Andersson, K K | [[Category: Andersson, K K]] | ||
[[Category: Hammerstad, M | [[Category: Hammerstad, M]] | ||
[[Category: Hersleth, H P | [[Category: Hersleth, H P]] | ||
[[Category: Rohr, A K | [[Category: Rohr, A K]] | ||
[[Category: Tomter, A B | [[Category: Tomter, A B]] | ||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
Revision as of 07:46, 25 December 2014
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)
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 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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