4lzb: Difference between revisions

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{{STRUCTURE_4lzb| PDB=4lzb | SCENE= }}
==Uracil binding pocket in Vaccinia virus uracil DNA glycosylase==
===Uracil binding pocket in Vaccinia virus uracil DNA glycosylase===
<StructureSection load='4lzb' size='340' side='right' caption='[[4lzb]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
{{ABSTRACT_PUBMED_24316823}}
== Structural highlights ==
<table><tr><td colspan='2'>[[4lzb]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LZB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LZB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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">[[4dof|4dof]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACAM3000_MVA_101, D4, MVA101R, UNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10245 Vaccinia virus])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </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=4lzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lzb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lzb RCSB], [http://www.ebi.ac.uk/pdbsum/4lzb PDBsum]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/UNG_VACCA UNG_VACCA]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Also part of a heterodimeric processivity factor which potentiates the DNA polymerase activity. Binds to DNA.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Poxvirus uracil DNA glycosylases are the most diverse members of the family I uracil DNA glycosylases (UNGs). The crystal structure of the uracil complex of Vaccinia virus uracil DNA glycosylase (D4) was determined at 2.03 A resolution. One uracil molecule was located in the active-site pocket in each of the 12 noncrystallographic symmetry-related D4 subunits. Although the UNGs of the poxviruses (including D4) feature significant differences in the characteristic motifs designated for uracil recognition and in the base-excision mechanism, the architecture of the active-site pocket in D4 is very similar to that in UNGs of other organisms. Overall, the interactions of the bound uracil with the active-site residues are also similar to the interactions previously observed in the structures of human and Escherichia coli UNG.


==Function==
Structure of the uracil complex of Vaccinia virus uracil DNA glycosylase.,Schormann N, Banerjee S, Ricciardi R, Chattopadhyay D Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Dec;69(Pt 12):1328-34., doi: 10.1107/S1744309113030613. Epub 2013 Nov 28. PMID:24316823<ref>PMID:24316823</ref>
[[http://www.uniprot.org/uniprot/UNG_VACCA UNG_VACCA]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Also part of a heterodimeric processivity factor which potentiates the DNA polymerase activity. Binds to DNA.  


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[4lzb]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LZB OCA].
</div>


==Reference==
==See Also==
<ref group="xtra">PMID:024316823</ref><references group="xtra"/><references/>
*[[Uracil-DNA glycosylase|Uracil-DNA glycosylase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Uracil-DNA glycosylase]]
[[Category: Uracil-DNA glycosylase]]
[[Category: Chattopadhyay, D.]]
[[Category: Vaccinia virus]]
[[Category: Schormann, N.]]
[[Category: Chattopadhyay, D]]
[[Category: Schormann, N]]
[[Category: A20]]
[[Category: A20]]
[[Category: Alpha/beta dna glycosylase fold]]
[[Category: Alpha/beta dna glycosylase fold]]
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