6cgn: Difference between revisions
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==X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound (pH 7)== | ==X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound (pH 7)== | ||
<StructureSection load='6cgn' size='340' side='right' caption='[[6cgn]], [[Resolution|resolution]] 2.26Å' scene=''> | <StructureSection load='6cgn' size='340' side='right'caption='[[6cgn]], [[Resolution|resolution]] 2.26Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6cgn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CGN OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6cgn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CGN 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]] 2.26Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D5M:2-DEOXYADENOSINE-5-MONOPHOSPHATE'>D5M</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6cgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cgn OCA], [https://pdbe.org/6cgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cgn RCSB], [https://www.ebi.ac.uk/pdbsum/6cgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cgn ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/RIR1_BACSU RIR1_BACSU] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity). | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 6cgn" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6cgn" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Bacillus subtilis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Boal AK]] | ||
[[Category: | [[Category: Maggiolo AO]] | ||
Latest revision as of 22:26, 29 May 2024
X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound (pH 7)X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound (pH 7)
Structural highlights
FunctionRIR1_BACSU Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity). 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. See AlsoReferences
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