This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
5x3g
From Proteopedia
(Difference between revisions)
| (One intermediate revision not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | The | + | ==The WT UNG crystal structure from Nitratifractor salsuginis== |
| + | <StructureSection load='5x3g' size='340' side='right' caption='[[5x3g]], [[Resolution|resolution]] 2.02Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5x3g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Nitse Nitse]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X3G FirstGlance]. <br> | ||
| + | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x3h|5x3h]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Nitsa_0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=749222 NITSE])</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=5x3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3g OCA], [http://pdbe.org/5x3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x3g RCSB], [http://www.ebi.ac.uk/pdbsum/5x3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3g ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity towards DNA base damage. Family 1 UNG exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginis UNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling and molecular dynamics simulations, shows that N. salsuginis UNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginis UNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution. This article is protected by copyright. All rights reserved. | ||
| - | + | An Unconventional Family 1 Uracil DNA Glycosylase in Nitratifractor salsuginis.,Li J, Chen R, Yang Y, Zhang Z, Fang GC, Xie W, Cao W FEBS J. 2017 Oct 4. doi: 10.1111/febs.14285. PMID:28977725<ref>PMID:28977725</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 5x3g" style="background-color:#fffaf0;"></div> |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Nitse]] | ||
[[Category: Cao, W]] | [[Category: Cao, W]] | ||
[[Category: Chen, R]] | [[Category: Chen, R]] | ||
[[Category: Xie, W]] | [[Category: Xie, W]] | ||
| + | [[Category: Zhang, Z]] | ||
| + | [[Category: Base excision repair]] | ||
| + | [[Category: Dna binding protein]] | ||
| + | [[Category: Single-wavelength anomalous dispersion]] | ||
| + | [[Category: Uracil dna glycosylase]] | ||
Current revision
The WT UNG crystal structure from Nitratifractor salsuginis
| |||||||||||
