3w5w: Difference between revisions
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==Mn2+-GMP complex of nanoRNase (Nrn) from Bacteroides fragilis== | ==Mn2+-GMP complex of nanoRNase (Nrn) from Bacteroides fragilis== | ||
<StructureSection load='3w5w' size='340' side='right'caption='[[3w5w]]' scene=''> | <StructureSection load='3w5w' size='340' side='right'caption='[[3w5w]], [[Resolution|resolution]] 2.95Å' 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=3W5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W5W FirstGlance]. <br> | <table><tr><td colspan='2'>[[3w5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis_YCH46 Bacteroides fragilis YCH46]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W5W FirstGlance]. <br> | ||
</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=3w5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5w OCA], [https://pdbe.org/3w5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w5w RCSB], [https://www.ebi.ac.uk/pdbsum/3w5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5w ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.95Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=3w5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5w OCA], [https://pdbe.org/3w5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w5w RCSB], [https://www.ebi.ac.uk/pdbsum/3w5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5w ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q64PD9_BACFR Q64PD9_BACFR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn(2)(+) ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins. | |||
Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins.,Uemura Y, Nakagawa N, Wakamatsu T, Kim K, Montelione GT, Hunt JF, Kuramitsu S, Masui R FEBS Lett. 2013 Aug 19;587(16):2669-74. doi: 10.1016/j.febslet.2013.06.053. Epub , 2013 Jul 9. PMID:23851074<ref>PMID:23851074</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3w5w" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacteroides fragilis YCH46]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Hunt JF]] | [[Category: Hunt JF]] | ||
Revision as of 12:51, 8 November 2023
Mn2+-GMP complex of nanoRNase (Nrn) from Bacteroides fragilis
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