2gv9: Difference between revisions

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[[Image:2gv9.png|left|200px]]


{{STRUCTURE_2gv9|  PDB=2gv9  |  SCENE=  }}
==Crystal structure of the Herpes Simplex virus type 1 DNA polymerase==
 
<StructureSection load='2gv9' size='340' side='right'caption='[[2gv9]], [[Resolution|resolution]] 2.68&Aring;' scene=''>
===Crystal structure of the Herpes Simplex virus type 1 DNA polymerase===
== Structural highlights ==
 
<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>
{{ABSTRACT_PUBMED_16638752}}
</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>
==About this Structure==
<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>
[[2gv9]] is a 2 chain structure of [[DNA polymerase]] with sequence 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].  
</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>


==See Also==
==See Also==
*[[DNA polymerase|DNA polymerase]]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
<ref group="xtra">PMID:016638752</ref><ref group="xtra">PMID:017997600</ref><references group="xtra"/>
[[Category: Human alphaherpesvirus 1 strain KOS]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Human herpesvirus 1]]
[[Category: Liu S]]
[[Category: Liu, S.]]
[[Category: Polymerase alpha fold]]
[[Category: Transferase]]

Latest revision as of 12:30, 14 February 2024

Crystal structure of the Herpes Simplex virus type 1 DNA polymeraseCrystal structure of the Herpes Simplex virus type 1 DNA polymerase

Structural highlights

2gv9 is a 2 chain structure with sequence from Human alphaherpesvirus 1 strain KOS. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.68Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2gv9, resolution 2.68Å

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