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.


4m3r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:23, 1 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==RB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex==
==RB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex==
-
<StructureSection load='4m3r' size='340' side='right' caption='[[4m3r]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
+
<StructureSection load='4m3r' size='340' side='right'caption='[[4m3r]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4m3r]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M3R FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4m3r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M3R FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.07&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4m3t|4m3t]], [[4m3u|4m3u]], [[4m3w|4m3w]], [[4m3x|4m3x]], [[4m3y|4m3y]], [[4m3z|4m3z]], [[4m41|4m41]], [[4m42|4m42]], [[4m45|4m45]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-
<tr id='gene'><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 BPR69])</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=4m3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m3r OCA], [https://pdbe.org/4m3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m3r RCSB], [https://www.ebi.ac.uk/pdbsum/4m3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m3r ProSAT]</span></td></tr>
-
<tr id='activity'><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 id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4m3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m3r OCA], [http://pdbe.org/4m3r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m3r RCSB], [http://www.ebi.ac.uk/pdbsum/4m3r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m3r ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
+
[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn2+ indicating that the tautomeric or ionization state of the base has changed. To see whether the tautomeric or ionization state of base-pair could be affect by its microenvironment, we determined ten structures of an RB69 DNA polymerase quadruple mutant with dG/dT or dT/dG mispairs at position n-1 to n-5 of the Primer/Template duplex. Different shapes of the mispairs, including Watson-Crick geometry, have been observed, strongly suggesting that the local environment of base-pairs plays an important role in their tautomeric or ionization states.
+
-
 
+
-
Mispairs with Watson-Crick Base-pair Geometry Observed in Ternary Complexes of an RB69 DNA Polymerase Variant.,Xia S, Konigsberg WH Protein Sci. 2014 Jan 24. doi: 10.1002/pro.2434. PMID:24458997<ref>PMID:24458997</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4m3r" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[DNA polymerase|DNA polymerase]]
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bpr69]]
+
[[Category: Escherichia phage RB69]]
-
[[Category: DNA-directed DNA polymerase]]
+
[[Category: Large Structures]]
-
[[Category: Konigsberg, W H]]
+
[[Category: Konigsberg WH]]
-
[[Category: Xia, S]]
+
[[Category: Xia S]]
-
[[Category: Dt/dg]]
+
-
[[Category: Hydrolase-dna complex]]
+
-
[[Category: N-1]]
+
-
[[Category: Quadruple]]
+
-
[[Category: Rb69]]
+
-
[[Category: Rb69 pol]]
+

Current revision

RB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex

PDB ID 4m3r

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/4m3r"
Personal tools