5x3g: Difference between revisions

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~~'''Unreleased structure'''~~

The ~~entry~~ 5x3g is ~~ON HOLD until Feb 06 2019~~

==The WT UNG crystal structure from Nitratifractor salsuginis==

== Structural highlights ==

<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='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='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='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>

</table>

== Function ==

[https://www.uniprot.org/uniprot/E6WYZ8_NITSE 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.

~~Authors: Xie, W~~., ~~Cao, W.~~, Chen, R., Zhang, Z.

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>

~~Description~~: ~~The WT UNG crystal structure from Nitratifractor salsuginis~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Zhang, Z~~]]

[[Category: Cao, W]]

[[Category: Chen, R]]

==See Also==

[[Category: Xie, W]]

*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Nitratifractor salsuginis DSM 16511]]

[[Category: Cao W]]

[[Category: Chen R]]

[[Category: Xie W]]

[[Category: Zhang Z]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5x3g is ON HOLD  until Feb 06 2019
+==The WT UNG crystal structure from Nitratifractor salsuginis==
+<StructureSection load='5x3g' size='340' side='right'caption='[[5x3g]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
+== Structural highlights ==
+<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.021&#8491;</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='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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/E6WYZ8_NITSE E6WYZ8_NITSE]
+<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.
-Authors: Xie, W., Cao, W., Chen, R., Zhang, Z.
+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>
-Description: The WT UNG crystal structure from Nitratifractor salsuginis
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Zhang, Z]]
+<div class="pdbe-citations 5x3g" style="background-color:#fffaf0;"></div>
-[[Category: Cao, W]]
-[[Category: Chen, R]]
+==See Also==
-[[Category: Xie, W]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Nitratifractor salsuginis DSM 16511]]
+[[Category: Cao W]]
+[[Category: Chen R]]
+[[Category: Xie W]]
+[[Category: Zhang Z]]