View source for 5grk


==Crystal structure of Uracil DNA glycosylase -Xanthine complex from Bradyrhizobium diazoefficiens==
<StructureSection load='5grk' size='340' side='right'caption='[[5grk]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5grk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GRK 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]] 2.804&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XAN:XANTHINE'>XAN</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=5grk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5grk OCA], [https://pdbe.org/5grk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5grk RCSB], [https://www.ebi.ac.uk/pdbsum/5grk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5grk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q89XR0_BRADU Q89XR0_BRADU] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
u: Repair of uracils in DNA is initiated by racil NA lycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 ( Bdi Ung) from Bradyrhizobium diazoefficiens . Although Bdi Ung contains the motif A (GQDPA), it has low sequence identity to known UDGs. Bdi Ung prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it. Bdi Ung is impervious to inhibition by AP DNA, and Ugi protein that specifically inhibits family 1 UDGs. Crystal structure of Bdi Ung shows similarity with the family 4 UDGs in its overall fold but with family 1 UDGs in key active site residues. However, instead of a classical motif B, Bdi Ung has a uniquely extended protrusion explaining the lack of Ugi inhibition. Structural and mutational analyses of Bdi Ung have revealed the basis for the accommodation of diverse substrates into its substrate binding pocket. Phylogenetically, Bdi Ung belongs to a new UDG family. Bradyrhizobium diazoefficiens presents a unique scenario where the presence of at least four families of UDGs may compensate for the absence of an efficient family 1 homologue.

Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity.,Chembazhi UV, Patil VV, Sah S, Reeve W, Tiwari RP, Woo E, Varshney U Nucleic Acids Res. 2017 Mar 28. doi: 10.1093/nar/gkx209. PMID:28369586<ref>PMID:28369586</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5grk" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bradyrhizobium diazoefficiens USDA 110]]
[[Category: Large Structures]]
[[Category: Ahn W]]
[[Category: Patil VV]]
[[Category: Ullas VC]]
[[Category: Varshney U]]
[[Category: Woo E]]