2vwk

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:01, 23 October 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2vwk.png|left|200px]]
 
-
<!--
+
==Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. V93Q polymerase variant==
-
The line below this paragraph, containing "STRUCTURE_2vwk", creates the "Structure Box" on the page.
+
<StructureSection load='2vwk' size='340' side='right'caption='[[2vwk]], [[Resolution|resolution]] 2.60&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'>[[2vwk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VWK 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]] 2.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_2vwk| PDB=2vwk | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwk OCA], [https://pdbe.org/2vwk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vwk RCSB], [https://www.ebi.ac.uk/pdbsum/2vwk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vwk ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
 +
== 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/vw/2vwk_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2vwk ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Archaeal family B DNA polymerases bind tightly to template-strand uracil and stall replication on encountering the pro-mutagenic base. This article describes an X-ray crystal structure, at 2.8 A resolution, of Thermococcus gorgonarius polymerase in complex with a DNA primer-template containing uracil in the single-stranded region. The DNA backbone is distorted to position the uracil deeply within a pocket, located in the amino-terminal domain of the polymerase. Specificity arises from a combination of hydrogen bonds between the protein backbone and uracil, with the pocket shaped to prevent the stable binding of the four standard DNA bases. Strong interactions are seen with the two phosphates that flank the uracil and the structure gives clues concerning the coupling of uracil binding to the halting of replication. The importance of key amino acids, identified by the analysis of the structure and their conservation between archaeal polymerases, was confirmed by site-directed mutagenesis. The crystal structure of V93Q, a polymerase variant that no longer recognises uracil, is also reported, explaining the V93Q phenotype by the steric exclusion of uracil from the pocket.
-
===URACIL RECOGNITION IN ARCHAEAL DNA POLYMERASES CAPTURED BY X-RAY CRYSTALLOGRAPHY. V93Q POLYMERASE VARIANT===
+
Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography.,Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA J Mol Biol. 2008 Sep 5;381(3):529-39. Epub 2008 Jun 7. PMID:18614176<ref>PMID:18614176</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2vwk" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18614176}}, 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 18614176 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18614176}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
2VWK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWK OCA].
+
-
 
+
-
==Reference==
+
-
Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography., Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA, J Mol Biol. 2008 Jun 7;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18614176 18614176]
+
-
[[Category: DNA-directed DNA polymerase]]
+
-
[[Category: Single protein]]
+
[[Category: Thermococcus gorgonarius]]
[[Category: Thermococcus gorgonarius]]
-
[[Category: Connolly, B A.]]
+
[[Category: Connolly BA]]
-
[[Category: Firbank, S J.]]
+
[[Category: Firbank SJ]]
-
[[Category: Heslop, P.]]
+
[[Category: Heslop P]]
-
[[Category: Lewis, R J.]]
+
[[Category: Lewis RJ]]
-
[[Category: Wardle, J.]]
+
[[Category: Wardle J]]
-
[[Category: Archaea]]
+
-
[[Category: Dna polymerase]]
+
-
[[Category: Dna repair]]
+
-
[[Category: Dna replication]]
+
-
[[Category: Dna-binding]]
+
-
[[Category: Dna-directed dna polymerase]]
+
-
[[Category: Exonuclease]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Multifunctional enzyme]]
+
-
[[Category: Nuclease]]
+
-
[[Category: Nucleotidyltransferase]]
+
-
[[Category: Transferase]]
+
-
[[Category: Uracil]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:29:45 2008''
+

Current revision

Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. V93Q polymerase variant

PDB ID 2vwk

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/2vwk"
Personal tools