6cgm: Difference between revisions
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<StructureSection load='6cgm' size='340' side='right' caption='[[6cgm]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='6cgm' size='340' side='right' caption='[[6cgm]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6cgm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CGM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CGM FirstGlance]. <br> | <table><tr><td colspan='2'>[[6cgm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CGM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CGM FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">B4417_3413, CFD21_09965 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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='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=6cgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cgm OCA], [http://pdbe.org/6cgm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cgm RCSB], [http://www.ebi.ac.uk/pdbsum/6cgm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cgm 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=6cgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cgm OCA], [http://pdbe.org/6cgm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cgm RCSB], [http://www.ebi.ac.uk/pdbsum/6cgm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cgm ProSAT]</span></td></tr> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Vibrio subtilis ehrenberg 1835]] | |||
[[Category: Ribonucleoside-diphosphate reductase]] | [[Category: Ribonucleoside-diphosphate reductase]] | ||
[[Category: Boal, A K]] | [[Category: Boal, A K]] | ||
Revision as of 10:46, 23 May 2018
X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit (nucleotide free)X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit (nucleotide free)
Structural highlights
Function[A0A162Q3J9_BACIU] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410] Publication Abstract from PubMedThe high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large alpha subunit and altering the enzyme's quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the alpha subunit of this RNR contains tightly bound deoxyadenosine 5'-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) alpha2 dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical alpha2 dimer is the predominant form of the dAMP-bound alpha in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical alpha2 inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner. An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP.,Parker MJ, Maggiolo AO, Thomas WC, Kim A, Meisburger SP, Ando N, Boal AK, Stubbe J Proc Natl Acad Sci U S A. 2018 Apr 30. pii: 1800356115. doi:, 10.1073/pnas.1800356115. PMID:29712847[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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