8un9: Difference between revisions
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==Crystal structure of the MrfB exonuclease catalytic core== | |||
<StructureSection load='8un9' size='340' side='right'caption='[[8un9]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8un9]] is a 2 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=8UN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8UN9 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.103Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=8un9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8un9 OCA], [https://pdbe.org/8un9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8un9 RCSB], [https://www.ebi.ac.uk/pdbsum/8un9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8un9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/YPRB_BACSU YPRB_BACSU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 A, in what appears to be an inactive state. In this conformation, a predicted alpha-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts. | |||
Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB.,Manthei KA, Munson LM, Nandakumar J, Simmons LA Nucleic Acids Res. 2024 Jun 24;52(11):6347-6359. doi: 10.1093/nar/gkae308. PMID:38661211<ref>PMID:38661211</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8un9" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis]] | |||
[[Category: Large Structures]] | |||
[[Category: Manthei KA]] | |||
[[Category: Nandakumar J]] | |||
[[Category: Simmons LA]] | |||
Latest revision as of 07:45, 3 July 2024
Crystal structure of the MrfB exonuclease catalytic core
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