This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3uiq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:3uiq.jpg|left|200px]]
+
==RB69 DNA Polymerase Ternary Complex containing dUpNpp==
 +
<StructureSection load='3uiq' size='340' side='right' caption='[[3uiq]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3uiq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UIQ FirstGlance]. <br>
 +
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene><br>
 +
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69])</td></tr>
 +
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
 +
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3uiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uiq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uiq RCSB], [http://www.ebi.ac.uk/pdbsum/3uiq PDBsum]</span></td></tr>
 +
<table>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Two divalent metal ions are required for primer-extension catalyzed by DNA polymerases. One metal ion brings the 3'-hydroxyl of the primer terminus and the alpha-phosphorus atom of incoming dNTP together for bond formation so that the catalytically relevant conformation of the triphosphate tail of the dNTP is in an alpha,beta,gamma-tridentate coordination complex with the second metal ion required for proper substrate alignment. A probable base selectivity mechanism derived from structural studies on Dpo4 suggests that the inability of mispaired dNTPs to form a substrate-aligned, tridentate coordination complex could effectively cause the mispaired dNTPs to be rejected before catalysis. Nevertheless, we found that mispaired dNTPs can actually form a properly aligned tridentate coordination complex. However, complementary dNTPs occasionally form misaligned complexes with mutant RB69 DNA polymerases (RB69pols) that are not in a tridentate coordination state. Here, we report finding a beta,gamma-bidentate coordination complex that contained the complementary dUpNpp opposite dA in the structure of a ternary complex formed by the wild type RB69pol at 1.88 A resolution. Our observations suggest that several distinct metal-ion coordination states can exist at the ground state in the polymerase active site and that base selectivity is unlikely to be based on metal-ion coordination alone.
-
<!--
+
Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase.,Xia S, Eom SH, Konigsberg WH, Wang J Protein Sci. 2012 Mar;21(3):447-51. doi: 10.1002/pro.2026. Epub 2012 Jan 31. PMID:22238207<ref>PMID:22238207</ref>
-
The line below this paragraph, containing "STRUCTURE_3uiq", creates the "Structure Box" on the page.
+
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
-
or leave the SCENE parameter empty for the default display.
+
-
-->
+
-
{{STRUCTURE_3uiq| PDB=3uiq | SCENE= }}
+
-
===RB69 DNA Polymerase Ternary Complex containing dUpNpp===
+
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
 +
</div>
-
 
+
==See Also==
-
<!--
+
*[[DNA polymerase|DNA polymerase]]
-
The line below this paragraph, {{ABSTRACT_PUBMED_22238207}}, adds the Publication Abstract to the page
+
== References ==
-
(as it appears on PubMed at http://www.pubmed.gov), where 22238207 is the PubMed ID number.
+
<references/>
-
-->
+
__TOC__
-
{{ABSTRACT_PUBMED_22238207}}
+
</StructureSection>
-
 
+
-
==About this Structure==
+
-
[[3uiq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UIQ OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:022238207</ref><references group="xtra"/>
+
[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Enterobacteria phage rb69]]
[[Category: Enterobacteria phage rb69]]

Revision as of 06:17, 5 June 2014

RB69 DNA Polymerase Ternary Complex containing dUpNpp

3uiq, resolution 1.88Å

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/3uiq"
Views
Personal tools
Navigation
Toolbox