6zjk: Difference between revisions
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==Ribonucleotide reductase R2 subunit from Clostridium botulinum== | ==Ribonucleotide reductase R2 subunit from Clostridium botulinum== | ||
<StructureSection load='6zjk' size='340' side='right'caption='[[6zjk]]' scene=''> | <StructureSection load='6zjk' size='340' side='right'caption='[[6zjk]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJK OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6zjk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clobm Clobm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZJK FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrdB, CLK_2200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=498214 CLOBM])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [https://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=6zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zjk OCA], [https://pdbe.org/6zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zjk RCSB], [https://www.ebi.ac.uk/pdbsum/6zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zjk ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[https://www.uniprot.org/uniprot/B1KYY8_CLOBM B1KYY8_CLOBM]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in Escherichia coli To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum, which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process. | |||
A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.,Martinez-Carranza M, Jonna VR, Lundin D, Sahlin M, Carlson LA, Jemal N, Hogbom M, Sjoberg BM, Stenmark P, Hofer A J Biol Chem. 2020 Nov 13;295(46):15576-15587. doi: 10.1074/jbc.RA120.014895. Epub, 2020 Sep 3. PMID:32883811<ref>PMID:32883811</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6zjk" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Clobm]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Martinez-Carranza M]] | [[Category: Ribonucleoside-diphosphate reductase]] | ||
[[Category: Stenmark P]] | [[Category: Martinez-Carranza, M]] | ||
[[Category: Stenmark, P]] | |||
[[Category: Metal binding protein]] | |||
[[Category: Nucleotide]] | |||
[[Category: R2]] | |||
[[Category: Reductase]] | |||
[[Category: Ribonucleotide]] | |||
Revision as of 09:55, 14 April 2021
Ribonucleotide reductase R2 subunit from Clostridium botulinumRibonucleotide reductase R2 subunit from Clostridium botulinum
Structural highlights
Function[B1KYY8_CLOBM] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[PIRNR:PIRNR000355] Publication Abstract from PubMedRibonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in Escherichia coli To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum, which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process. A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.,Martinez-Carranza M, Jonna VR, Lundin D, Sahlin M, Carlson LA, Jemal N, Hogbom M, Sjoberg BM, Stenmark P, Hofer A J Biol Chem. 2020 Nov 13;295(46):15576-15587. doi: 10.1074/jbc.RA120.014895. Epub, 2020 Sep 3. PMID:32883811[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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