6lyd: Difference between revisions
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<StructureSection load='6lyd' size='340' side='right'caption='[[6lyd]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='6lyd' size='340' side='right'caption='[[6lyd]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6lyd]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6lyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus] and [https://en.wikipedia.org/wiki/Bacillus_phage_PBS2 Bacillus phage PBS2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LYD 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]] 2.598Å</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=6lyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lyd OCA], [https://pdbe.org/6lyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lyd RCSB], [https://www.ebi.ac.uk/pdbsum/6lyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lyd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/UNG_MIMIV UNG_MIMIV] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. | ||
<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 6lyd" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6lyd" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Uracil glycosylase inhibitor|Uracil glycosylase inhibitor]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Acanthamoeba polyphaga mimivirus]] | ||
[[Category: | [[Category: Bacillus phage PBS2]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Kim | [[Category: Kim DY]] | ||
[[Category: Kwon | [[Category: Kwon E]] | ||
[[Category: Pathak | [[Category: Pathak D]] | ||
Latest revision as of 18:03, 29 November 2023
Crystal Structure of mimivirus UNG Y322L in complex with UGICrystal Structure of mimivirus UNG Y322L in complex with UGI
Structural highlights
FunctionUNG_MIMIV Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Publication Abstract from PubMedUracil-N-glycosylase (UNG) is found in most organisms as well as in large DNA viruses. Its inhibitory proteins, including uracil glycosylase inhibitor (UGI) and p56, tightly bind to the active site of UNG by mimicking the DNA substrates. As the binding motifs are conserved in UNG family proteins, the inhibitory proteins bind to various UNG proteins across species. However, the intercalation residue that penetrates the DNA minor groove during uracil excision is not conserved among UNG proteins. To understand the role of the intercalation residue in their binding to the inhibitory proteins, we prepared mutants of mimivirus UNG, measured the binding affinity between the UNG mutants and inhibitory proteins, and analyzed the interactions based on the crystal structures of mimivirus UNG mutants complexed with UGI. The results show that mimivirus UNG, which harbors Tyr as an intercalation residue, did not interact with the inhibitory proteins intrinsically, whereas mutations of the intercalation residue to Phe or Leu resulted in tight interactions with UGI and p56; mutation to Met resulted in tight interactions only with p56. The crystal structures revealed that Phe and Leu stabilize the interactions by fitting into the hydrophobic pocket of UGI. These results show that differences in size and hydrophobicity of the intercalation residues determine the interactions between UNG family proteins and the inhibitory proteins, UGI and p56. Selective interactions between mimivirus uracil-DNA glycosylase and inhibitory proteins determined by a single amino acid.,Pathak D, Kwon E, Young Kim D J Struct Biol. 2020 Jun 19:107552. doi: 10.1016/j.jsb.2020.107552. PMID:32569642[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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