2owq

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(New page: 200px<br /><applet load="2owq" size="350" color="white" frame="true" align="right" spinBox="true" caption="2owq, resolution 2.40&Aring;" /> '''Crystal structure of...)
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[[Image:2owq.jpg|left|200px]]<br /><applet load="2owq" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2owq, resolution 2.40&Aring;" />
 
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'''Crystal structure of vaccinia virus uracil-DNA glycosylase'''<br />
 
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==Overview==
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==Crystal structure of vaccinia virus uracil-DNA glycosylase==
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ABSTRACT: BACKGROUND: Uracil-DNA glycosylases (UDGs) catalyze excision of, uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of, other organisms in primary, secondary and tertiary structure and, characteristic motifs. It adopted a novel catalysis-independent role in, DNA replication that involves interaction with a viral protein, A20, to, form the processivity factor. UDG:A20 association is essential for, assembling of the processive DNA polymerase complex. The structure of the, protein must have provisions for such interactions with A20. This paper, provides the first glimpse into the structure of a poxvirus UDG. RESULTS:, Results of dynamic light scattering experiments and native size exclusion, chromatography showed that vvUDG is a dimer in solution. The dimeric, assembly is also maintained in two crystal forms. The core of vvUDG is, reasonably well conserved but the structure contains one additional, beta-sheet at each terminus. A glycerol molecule is found in the active, site of the enzyme in both crystal forms. Interaction of this glycerol, molecule with the protein possibly mimics the enzyme-substrate (uracil), interactions. CONCLUSIONS: The crystal structures reveal several, distinctive features of vvUDG. The new structural features may have, evolved for adopting novel functions in the replication machinery of, poxviruses. The mode of interaction between the subunits in the dimers, suggests a possible model for binding to its partner and the nature of the, processivity factor in the polymerase complex.
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<StructureSection load='2owq' size='340' side='right'caption='[[2owq]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2owq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_Western_Reserve Vaccinia virus Western Reserve]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OWQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OWQ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2owq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2owq OCA], [https://pdbe.org/2owq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2owq RCSB], [https://www.ebi.ac.uk/pdbsum/2owq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2owq ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/UNG_VACCW UNG_VACCW] 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 (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ow/2owq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2owq ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2OWQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=IMD:'>IMD</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OWQ OCA].
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly., Schorman N, Grigorian A, Samal A, Krishnan R, Delucas L, Chattopadhyay D, BMC Struct Biol. 2007 Jul 2;7(1):45. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17605817 17605817]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Vaccinia virus Western Reserve]]
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[[Category: Vaccinia virus]]
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[[Category: Chattopadhyay D]]
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[[Category: Chattopadhyay, D.]]
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[[Category: Schormann N]]
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[[Category: Schormann, N.]]
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[[Category: CL]]
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[[Category: GOL]]
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[[Category: IMD]]
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[[Category: SO4]]
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[[Category: and parallel beta-sheet of 4 strands in the order 2134; novel features: beta-sheets at n- and c-terminus]]
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[[Category: uracil-dna glycosylase fold in the core: 3 layers (a/b/a)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:49:36 2008''
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Current revision

Crystal structure of vaccinia virus uracil-DNA glycosylase

PDB ID 2owq

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