2kxe: Difference between revisions

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{{Seed}}
[[Image:2kxe.jpg|left|200px]]


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==N-terminal domain of the DP1 subunit of an archaeal D-family DNA polymerase==
The line below this paragraph, containing "STRUCTURE_2kxe", creates the "Structure Box" on the page.
<StructureSection load='2kxe' size='340' side='right'caption='[[2kxe]]' 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'>[[2kxe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KXE 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">Solution NMR</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=2kxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kxe OCA], [https://pdbe.org/2kxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kxe RCSB], [https://www.ebi.ac.uk/pdbsum/2kxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kxe ProSAT]</span></td></tr>
{{STRUCTURE_2kxe|  PDB=2kxe  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/DP2S_PYRHO DP2S_PYRHO] Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3' to 5' direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (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/kx/2kxe_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=2kxe ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Archaea-specific D-family DNA polymerase forms a heterotetramer consisting of two large polymerase subunits and two small exonuclease subunits. We analyzed the structure of the N-terminal 200 amino-acid regulatory region of the small subunit by NMR and revealed that the N-terminal approximately 70 amino-acid region is folded. The structure consists of a four-alpha-helix bundle including a short parallel beta-sheet, which is similar to the N-terminal regions of the B subunits of human DNA polymerases alpha and epsilon, establishing evolutionary relationships among these archaeal and eukaryotic polymerases. We observed monomer-dimer equilibrium of this domain, which may be related to holoenzyme architecture and/or functional regulation.


===N-terminal domain of the DP1 subunit of an archaeal D-family DNA polymerase===
Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases.,Yamasaki K, Urushibata Y, Yamasaki T, Arisaka F, Matsui I FEBS Lett. 2010 Aug 4;584(15):3370-5. Epub 2010 Jun 23. PMID:20598295<ref>PMID:20598295</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2kxe" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_20598295}}, adds the Publication Abstract to the page
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 20598295 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20598295}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2KXE is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KXE OCA].
 
==Reference==
<ref group="xtra">PMID:20598295</ref><references group="xtra"/>
[[Category: DNA-directed DNA polymerase]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
[[Category: Matsui, I.]]
[[Category: Matsui I]]
[[Category: Yamasaki, K.]]
[[Category: Yamasaki K]]
[[Category: Archara]]
[[Category: D-family]]
[[Category: Dna polymerase]]
[[Category: Helical bundle]]
[[Category: Small subunit]]
[[Category: Transferase]]
 
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Retrieved from "https://proteopedia.org/2kxe"