3o59

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 3: Line 3:
<StructureSection load='3o59' size='340' side='right'caption='[[3o59]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3o59' size='340' side='right'caption='[[3o59]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3o59]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O59 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3o59]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O59 FirstGlance]. <br>
-
</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>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0121 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=3o59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o59 OCA], [https://pdbe.org/3o59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o59 RCSB], [https://www.ebi.ac.uk/pdbsum/3o59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o59 ProSAT]</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=3o59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o59 OCA], [https://pdbe.org/3o59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o59 RCSB], [https://www.ebi.ac.uk/pdbsum/3o59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o59 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/DP2L_PYRHO DP2L_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).
+
[https://www.uniprot.org/uniprot/DP2L_PYRHO DP2L_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).
-
<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. The N-terminal (1-300) domain structure of the large subunit was determined by X-ray crystallography, although approximately 50 N-terminal residues were disordered. The determined structure consists of nine alpha helices and three beta strands. We also identified the DNA-binding ability of the domain by SPR measurement. The N-terminal (1-100) region plays crucial roles in the folding of the large subunit dimer by connecting the approximately 50 N-terminal residues with their own catalytic region (792-1163). STRUCTURED SUMMARY: DP2binds to DP2 by molecular sieving(View interaction) DP2binds to DP2 by fluorescence technology(View interaction) DP2binds to DP2 by circular dichroism(View interaction).
+
-
Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii.,Matsui I, Urushibata Y, Shen Y, Matsui E, Yokoyama H FEBS Lett. 2011 Feb 4;585(3):452-8. Epub 2010 Dec 28. PMID:21192935<ref>PMID:21192935</ref>
+
==See Also==
-
 
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3o59" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Pyrococcus shinkaii]]
 
-
[[Category: DNA-directed DNA polymerase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Matsui, I]]
+
[[Category: Pyrococcus horikoshii]]
-
[[Category: Shen, Y]]
+
[[Category: Matsui I]]
-
[[Category: Yokoyama, H]]
+
[[Category: Shen Y]]
-
[[Category: Alpha helical structure]]
+
[[Category: Yokoyama H]]
-
[[Category: Dna polymerase]]
+
-
[[Category: Transferase]]
+

Revision as of 10:03, 14 February 2024

DNA polymerase D large subunit DP2(1-300) from Pyrococcus horikoshii

PDB ID 3o59

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3o59"
Personal tools