2z0l: Difference between revisions

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-[[Image:2z0l.png|left|200px]]
-{{STRUCTURE_2z0l|  PDB=2z0l  |  SCENE=  }}
+==Crystal structure of EBV-DNA polymerase accessory protein BMRF1==
+<StructureSection load='2z0l' size='340' side='right'caption='[[2z0l]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2z0l]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ebvb9 Ebvb9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z0L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Z0L FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2z0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z0l OCA], [http://pdbe.org/2z0l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z0l RCSB], [http://www.ebi.ac.uk/pdbsum/2z0l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z0l ProSAT], [http://www.topsan.org/Proteins/RSGI/2z0l TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/EAD_EBVB9 EAD_EBVB9]] Plays an essential role in the viral lytic DNA replication by acting as the polymerase accessory subunit. Stimulates the viral DNA polymerase activity and appears to function with it as a holoenzyme. Increases the processivity of the viral polymerase, probably by acting as a sliding clamp that prevents dissociation of the polymerase from the active template. In addition, BMRF1 transcriptionally activates the early BHLF1 promoter.<ref>PMID:16641300</ref> <ref>PMID:8764021</ref>
+== 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/z0/2z0l_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/main_output.php?pdb_ID=2z0l ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The DNA polymerase processivity factor of the Epstein-Barr virus, BMRF1, associates with the polymerase catalytic subunit, BALF5, to enhance the polymerase processivity and exonuclease activities of the holoenzyme. In this study, the crystal structure of C-terminally truncated BMRF1 (BMRF1-DeltaC) was solved in an oligomeric state. The molecular structure of BMRF1-DeltaC shares structural similarity with other processivity factors, such as herpes simplex virus UL42, cytomegalovirus UL44, and human proliferating cell nuclear antigen. However, the oligomerization architectures of these proteins range from a monomer to a trimer. PAGE and mutational analyses indicated that BMRF1-DeltaC, like UL44, forms a C-shaped head-to-head dimer. DNA binding assays suggested that basic amino acid residues on the concave surface of the C-shaped dimer play an important role in interactions with DNA. The C95E mutant, which disrupts dimer formation, lacked DNA binding activity, indicating that dimer formation is required for DNA binding. These characteristics are similar to those of another dimeric viral processivity factor, UL44. Although the R87E and H141F mutants of BMRF1-DeltaC exhibited dramatically reduced polymerase processivity, they were still able to bind DNA and to dimerize. These amino acid residues are located near the dimer interface, suggesting that BMRF1-DeltaC associates with the catalytic subunit BALF5 around the dimer interface. Consequently, the monomeric form of BMRF1-DeltaC probably binds to BALF5, because the steric consequences would prevent the maintenance of the dimeric form. A distinctive feature of BMRF1-DeltaC is that the dimeric and monomeric forms might be utilized for the DNA binding and replication processes, respectively.
-===Crystal structure of EBV-DNA polymerase accessory protein BMRF1===
+Crystal structure of epstein-barr virus DNA polymerase processivity factor BMRF1.,Murayama K, Nakayama S, Kato-Murayama M, Akasaka R, Ohbayashi N, Kamewari-Hayami Y, Terada T, Shirouzu M, Tsurumi T, Yokoyama S J Biol Chem. 2009 Dec 18;284(51):35896-905. Epub . PMID:19801550<ref>PMID:19801550</ref>
-{{ABSTRACT_PUBMED_19801550}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2z0l" style="background-color:#fffaf0;"></div>
-[[2z0l]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_4 Human herpesvirus 4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z0L OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:019801550</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Human herpesvirus 4]]
+[[Category: Ebvb9]]
-[[Category: Kato-Murayama, M.]]
+[[Category: Large Structures]]
-[[Category: Murayama, K.]]
+[[Category: Kato-Murayama, M]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Murayama, K]]
-[[Category: Shirouzu, M.]]
+[[Category: Structural genomic]]
-[[Category: Terada, T.]]
+[[Category: Shirouzu, M]]
-[[Category: Yokoyama, S.]]
+[[Category: Terada, T]]
+[[Category: Yokoyama, S]]
 [[Category: Activator]]
 [[Category: Alpha/beta protein]]
@@ Line 27: / Line 49: @@
 [[Category: Nucleus]]
 [[Category: Replication]]
-[[Category: Riken structural genomics/proteomics initiative]]
 [[Category: Rsgi]]
-[[Category: Structural genomic]]
 [[Category: Transcription]]
 [[Category: Transcription regulation]]