2gv9: Difference between revisions

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-{{Seed}}
-[[Image:2gv9.png|left|200px]]
-<!--
+==Crystal structure of the Herpes Simplex virus type 1 DNA polymerase==
-The line below this paragraph, containing "STRUCTURE_2gv9", creates the "Structure Box" on the page.
+<StructureSection load='2gv9' size='340' side='right'caption='[[2gv9]], [[Resolution|resolution]] 2.68&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2gv9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_KOS Human alphaherpesvirus 1 strain KOS]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GV9 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.68&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2gv9|  PDB=2gv9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gv9 OCA], [https://pdbe.org/2gv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gv9 RCSB], [https://www.ebi.ac.uk/pdbsum/2gv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gv9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOL_HHV1K DPOL_HHV1K] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (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/gv/2gv9_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=2gv9 ConSurf].
+<div style="clear:both"></div>
-===Crystal structure of the Herpes Simplex virus type 1 DNA polymerase===
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+__TOC__
-<!--
+</StructureSection>
-The line below this paragraph, {{ABSTRACT_PUBMED_16638752}}, adds the Publication Abstract to the page
+[[Category: Human alphaherpesvirus 1 strain KOS]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16638752 is the PubMed ID number.
+[[Category: Large Structures]]
--->
+[[Category: Liu S]]
-{{ABSTRACT_PUBMED_16638752}}
-==About this Structure==
-GV9 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GV9 OCA].
-==Reference==
-<ref group="xtra">PMID:16638752</ref><references group="xtra"/>
-[[Category: DNA-directed DNA polymerase]]
-[[Category: Human herpesvirus 1]]
-[[Category: Liu, S.]]
-[[Category: Polymerase alpha fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:30:55 2009''