5gnw: Difference between revisions

Latest revision as of 11:37, 2 August 2023

Crystal structure of Uracil DNA glycosylase-Uracil complex from Bradyrhizobium diazoefficiens.

Structural highlights

5gnw is a 8 chain structure with sequence from Bradyrhizobium diazoefficiens USDA 110. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.869Å
Ligands:	MSE, URA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q89XR0_BRADU

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^[1]

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

References

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

[1]

@@ Line 1: / Line 1: @@
 ==Crystal structure of Uracil DNA glycosylase-Uracil complex from Bradyrhizobium diazoefficiens.==
-<StructureSection load='5gnw' size='340' side='right' caption='[[5gnw]], [[Resolution|resolution]] 2.87&Aring;' scene=''>
+<StructureSection load='5gnw' size='340' side='right'caption='[[5gnw]], [[Resolution|resolution]] 2.87&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gnw]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradu Bradu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GNW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GNW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gnw]] is a 8 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=5GNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GNW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=URA:URACIL'>URA</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]] 2.869&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gn2|5gn2]], [[5gn3|5gn3]]</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=5gnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gnw OCA], [https://pdbe.org/5gnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gnw RCSB], [https://www.ebi.ac.uk/pdbsum/5gnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gnw ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">blr0248 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224911 BRADU])</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=5gnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gnw OCA], [http://pdbe.org/5gnw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gnw RCSB], [http://www.ebi.ac.uk/pdbsum/5gnw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gnw ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q89XR0_BRADU Q89XR0_BRADU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5gnw" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bradu]]
+[[Category: Bradyrhizobium diazoefficiens USDA 110]]
-[[Category: Chembazhi, U V]]
+[[Category: Large Structures]]
-[[Category: Patil, V V]]
+[[Category: Chembazhi UV]]
-[[Category: Varshney, U]]
+[[Category: Patil VV]]
-[[Category: Woo, E]]
+[[Category: Varshney U]]
-[[Category: Bradyrhizobium diazoefficien]]
+[[Category: Woo E]]
-[[Category: Dna repair]]
-[[Category: Hydrolase]]

5gnw: Difference between revisions

Latest revision as of 11:37, 2 August 2023

Crystal structure of Uracil DNA glycosylase-Uracil complex from Bradyrhizobium diazoefficiens.

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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