2m2v: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{STRUCTURE_2m2v|  PDB=2m2v  |  SCENE=  }}
-===African Swine Fever Virus Pol X in the ternary complex with MgdGTP and DNA===
-{{ABSTRACT_PUBMED_24617852}}
-==Function==
+==African Swine Fever Virus Pol X in the ternary complex with MgdGTP and DNA==
-[[http://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7]] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>
+<StructureSection load='2m2v' size='340' side='right'caption='[[2m2v]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2m2v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/African_swine_fever_virus African swine fever virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M2V FirstGlance]. <br>
+</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=2m2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m2v OCA], [https://pdbe.org/2m2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m2v RCSB], [https://www.ebi.ac.uk/pdbsum/2m2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m2v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix alphaE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.
-==About this Structure==
+How a Low-Fidelity DNA Polymerase Chooses Non-Watson-Crick from Watson-Crick Incorporation.,Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW, Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai MD J Am Chem Soc. 2014 Mar 21. PMID:24617852<ref>PMID:24617852</ref>
-[[2m2v]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M2V OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:024617852</ref><references group="xtra"/><references/>
+</div>
-[[Category: DNA-directed DNA polymerase]]
+<div class="pdbe-citations 2m2v" style="background-color:#fffaf0;"></div>
-[[Category: Su, M.]]
-[[Category: Tsai, M.]]
+==See Also==
-[[Category: Wu, W.]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-[[Category: Dna polymerase]]
+== References ==
-[[Category: Nucleotidyl transferase]]
+<references/>
-[[Category: Transferase]]
+__TOC__
+</StructureSection>
+[[Category: African swine fever virus]]
+[[Category: Large Structures]]
+[[Category: Su M]]
+[[Category: Tsai M]]
+[[Category: Wu W]]