1jqr

From Proteopedia

(Difference between revisions)

Current revision

NMR structure of the African swine fever virus DNA polymerase X

Structural highlights

1jqr is a 1 chain structure with sequence from African swine fever virus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 21 models
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The African swine fever virus DNA polymerase X (ASFV Pol X or Pol X), the smallest known nucleotide polymerase, has recently been reported to be an extremely low fidelity polymerase that may be involved in strategic mutagenesis of the viral genome. Here we report the solution structure of Pol X. The structure, unique within the realm of nucleotide polymerases, consists of only palm and fingers subdomains. Despite the absence of a thumb subdomain, which is important for DNA binding in other polymerases, we show that Pol X binds DNA with very high affinity. Further structural analyses suggest a novel mode of DNA binding that may contribute to low fidelity synthesis. We also demonstrate that the ASFV DNA ligase is a low fidelity ligase capable of sealing a nick that contains a G-G mismatch. This supports the hypothesis of a virus-encoded, mutagenic base excision repair pathway consisting of a tandem Pol X/ligase mutator.

Solution structure of a viral DNA polymerase X and evidence for a mutagenic function.,Showalter AK, Byeon IJ, Su MI, Tsai MD Nat Struct Biol. 2001 Nov;8(11):942-6. PMID:11685239^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Garcia-Escudero R, Garcia-Diaz M, Salas ML, Blanco L, Salas J. DNA polymerase X of African swine fever virus: insertion fidelity on gapped DNA substrates and AP lyase activity support a role in base excision repair of viral DNA. J Mol Biol. 2003 Mar 7;326(5):1403-12. PMID:12595253
↑ Showalter AK, Byeon IJ, Su MI, Tsai MD. Solution structure of a viral DNA polymerase X and evidence for a mutagenic function. Nat Struct Biol. 2001 Nov;8(11):942-6. PMID:11685239 doi:10.1038/nsb1101-942
↑ Showalter AK, Byeon IJ, Su MI, Tsai MD. Solution structure of a viral DNA polymerase X and evidence for a mutagenic function. Nat Struct Biol. 2001 Nov;8(11):942-6. PMID:11685239 doi:10.1038/nsb1101-942

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1jqr"

@@ Line 1: / Line 1: @@
 ==NMR structure of the African swine fever virus DNA polymerase X==
-<StructureSection load='1jqr' size='340' side='right' caption='[[1jqr]], [[NMR_Ensembles_of_Models | 21 NMR models]]' scene=''>
+<StructureSection load='1jqr' size='340' side='right'caption='[[1jqr]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1jqr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Asf Asf]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JQR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1jqr]] 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=1JQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JQR FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">O174L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10497 ASF])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 21 models</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [http://pdbe.org/1jqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [http://www.ebi.ac.uk/pdbsum/1jqr PDBsum]</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=1jqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqr OCA], [https://pdbe.org/1jqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jqr RCSB], [https://www.ebi.ac.uk/pdbsum/1jqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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>
+[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>
 == 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/jq/1jqr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jq/1jqr_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 27: / Line 28: @@
 </div>
 <div class="pdbe-citations 1jqr" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Methane monooxygenase|Methane monooxygenase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Asf]]
+[[Category: African swine fever virus]]
-[[Category: Byeon, I J.L]]
+[[Category: Large Structures]]
-[[Category: Showalter, A K]]
+[[Category: Byeon I-JL]]
-[[Category: Su, M I]]
+[[Category: Showalter AK]]
-[[Category: Tsai, M D]]
+[[Category: Su M-I]]
-[[Category: Dna polymerase]]
+[[Category: Tsai M-D]]
-[[Category: Viral protein]]

1jqr

From Proteopedia

Current revision

NMR structure of the African swine fever virus DNA polymerase X

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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