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| | ==The WT UNG crystal structure from Nitratifractor salsuginis== | | ==The WT UNG crystal structure from Nitratifractor salsuginis== |
| - | <StructureSection load='5x3g' size='340' side='right' caption='[[5x3g]], [[Resolution|resolution]] 2.02Å' scene=''> | + | <StructureSection load='5x3g' size='340' side='right'caption='[[5x3g]], [[Resolution|resolution]] 2.02Å' scene=''> |
| | == Structural highlights == | | == 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> | + | <table><tr><td colspan='2'>[[5x3g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nitratifractor_salsuginis_DSM_16511 Nitratifractor salsuginis DSM 16511]. 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 [https://proteopedia.org/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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.021Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x3h|5x3h]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5x3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x3g OCA], [https://pdbe.org/5x3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x3g RCSB], [https://www.ebi.ac.uk/pdbsum/5x3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x3g ProSAT]</span></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> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/E6WYZ8_NITSE E6WYZ8_NITSE] |
| | <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 5x3g" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5x3g" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Nitse]] | + | [[Category: Large Structures]] |
| - | [[Category: Cao, W]] | + | [[Category: Nitratifractor salsuginis DSM 16511]] |
| - | [[Category: Chen, R]] | + | [[Category: Cao W]] |
| - | [[Category: Xie, W]] | + | [[Category: Chen R]] |
| - | [[Category: Zhang, Z]] | + | [[Category: Xie W]] |
| - | [[Category: Base excision repair]]
| + | [[Category: Zhang Z]] |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Single-wavelength anomalous dispersion]]
| + | |
| - | [[Category: Uracil dna glycosylase]]
| + | |
| Structural highlights
Function
E6WYZ8_NITSE
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Li J, Chen R, Yang Y, Zhang Z, Fang GC, Xie W, Cao W. An Unconventional Family 1 Uracil DNA Glycosylase in Nitratifractor salsuginis. FEBS J. 2017 Oct 4. doi: 10.1111/febs.14285. PMID:28977725 doi:http://dx.doi.org/10.1111/febs.14285
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