3n4p: Difference between revisions

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 ==Human cytomegalovirus terminase nuclease domain==
-<StructureSection load='3n4p' size='340' side='right' caption='[[3n4p]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+<StructureSection load='3n4p' size='340' side='right'caption='[[3n4p]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3n4p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_5 Human herpesvirus 5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N4P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3n4p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_herpesvirus_5_strain_Towne Human herpesvirus 5 strain Towne]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N4P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.15&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3n4q|3n4q]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3n4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n4p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n4p RCSB], [http://www.ebi.ac.uk/pdbsum/3n4p PDBsum]</span></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=3n4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n4p OCA], [https://pdbe.org/3n4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n4p RCSB], [https://www.ebi.ac.uk/pdbsum/3n4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n4p ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRM3_HCMVA TRM3_HCMVA] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n4/3n4p_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n4/3n4p_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3n4p ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-During viral replication, herpesviruses package their DNA into the procapsid by means of the terminase protein complex. In human cytomegalovirus (herpesvirus 5), the terminase is composed of subunits UL89 and UL56. UL89 cleaves the long DNA concatemers into unit-length genomes of appropriate length for encapsidation. We used ESPRIT, a high-throughput screening method, to identify a soluble purifiable fragment of UL89 from a library of 18,432 randomly truncated ul89 DNA constructs. The purified protein was crystallized and its three-dimensional structure was solved. This protein corresponds to the key nuclease domain of the terminase and shows an RNase H/integrase-like fold. We demonstrate that UL89-C has the capacity to process the DNA and that this function is dependent on Mn(2+) ions, two of which are located at the active site pocket. We also show that the nuclease function can be inactivated by raltegravir, a recently approved anti-AIDS drug that targets the HIV integrase.
-Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain.,Nadal M, Mas PJ, Blanco AG, Arnan C, Sola M, Hart DJ, Coll M Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16078-83. Epub 2010 Aug 30. PMID:20805464<ref>PMID:20805464</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Terminase 3D Structures|Terminase 3D Structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Human herpesvirus 5]]
+[[Category: Human herpesvirus 5 strain Towne]]
-[[Category: Arnan, C]]
+[[Category: Large Structures]]
-[[Category: Blanco, A G]]
+[[Category: Arnan C]]
-[[Category: Coll, M]]
+[[Category: Blanco AG]]
-[[Category: Hart, D J]]
+[[Category: Coll M]]
-[[Category: Mas, P J]]
+[[Category: Hart DJ]]
-[[Category: Nadal, M]]
+[[Category: Mas PJ]]
-[[Category: Sola, M]]
+[[Category: Nadal M]]
-[[Category: Dna binding protein]]
+[[Category: Sola M]]
-[[Category: Dna packaging]]
-[[Category: Hcmv]]
-[[Category: Herpesvirus]]
-[[Category: Human cytomegalovirus]]
-[[Category: Nuclease]]
-[[Category: Terminase]]