Structure of Human DNA Polymerase κ Inserting dATP Opposite an 8-OxoG DNA Lesion
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{"title"=>"Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion", "type"=>"journal", "authors"=>[{"first_name"=>"Rodrigo", "last_name"=>"Vasquez-Del Carpio", "scopus_author_id"=>"10641746100"}, {"first_name"=>"Timothy D.", "last_name"=>"Silverstein", "scopus_author_id"=>"26645210500"}, {"first_name"=>"Samer", "last_name"=>"Lone", "scopus_author_id"=>"15925399400"}, {"first_name"=>"Michael K.", "last_name"=>"Swan", "scopus_author_id"=>"57197944569"}, {"first_name"=>"Jayati R.", "last_name"=>"Choudhury", "scopus_author_id"=>"9038612000"}, {"first_name"=>"Robert E.", "last_name"=>"Johnson", "scopus_author_id"=>"57126573500"}, {"first_name"=>"Satya", "last_name"=>"Prakash", "scopus_author_id"=>"7202838645"}, {"first_name"=>"Louise", "last_name"=>"Prakash", "scopus_author_id"=>"7102772462"}, {"first_name"=>"Aneel K.", "last_name"=>"Aggarwal", "scopus_author_id"=>"7201563903"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"66849126006", "doi"=>"10.1371/journal.pone.0005766", "pui"=>"354709481", "pmid"=>"19492058", "scopus"=>"2-s2.0-66849126006", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"ba9c051f-4fac-340e-9b2b-206be2f8db17", "abstract"=>"Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase kappa (Polkappa) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polkappa's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polkappa in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide.", "link"=>"http://www.mendeley.com/research/structure-human-dna-polymerase-%CE%BA-inserting-datp-opposite-8oxog-dna-lesion", "reader_count"=>26, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Researcher"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Researcher"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>9, "Physics and Astronomy"=>1, "Chemistry"=>8}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>8}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Germany"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/895938/Figure_1.tif"], "description"=>"<p>(A) Ribbon diagram representing the overall structure of the ternary complex. The palm, fingers, thumb, PAD and N-clasp domains are shown in cyan, yellow, orange, green, and blue, respectively. DNA is shown in gray and the 8-oxoG lesion and incoming dATP are shown in red. A putative Mg<sup>2+</sup> ion is shown as a yellow sphere. (B) A view of the ternary complex looking down the DNA helix to show encirclement of the adducted DNA by the N-clasp. (C) Simulated annealing Fo-Fc omit map (contoured at 3.5σ) of 8-oxoG and incoming dATP.</p>", "links"=>[], "tags"=>["ternary"], "article_id"=>566385, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Rodrigo Vasquez-Del Carpio", "Timothy D. Silverstein", "Samer Lone", "Michael K. Swan", "Jayati R. Choudhury", "Robert E. Johnson", "Satya Prakash", "Louise Prakash", "Aneel K. Aggarwal"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0005766.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Pol_954_8_oxoG_dATP_ternary_complex_/566385", "title"=>"Polκ/8-oxoG/dATP ternary complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:45:23"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/896033/Figure_2.tif"], "description"=>"<p>(A) Close-up view of the Polκ active site cleft. Highlighted and labeled are the catalytic residues (D107, D198, and E199), residues apposed close to incoming dATP (Y112, T138, R144, Y141, and K328), 8-oxoG (M135 and A151), and the base 5<i>′</i> to 8-oxoG (F49 and P153). A putative Mg<sup>2+</sup> ion is shown as a yellow sphere. (B) Molecular surface representation of the Polκ active site cleft. Highlighted in gray and labeled are residues apposed close to 8-oxoG and the base 5′ to it. A putative Mg<sup>2+</sup> ion is shown as a yellow sphere.</p>", "links"=>[], "tags"=>["pairing", "incoming"], "article_id"=>566487, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Rodrigo Vasquez-Del Carpio", "Timothy D. Silverstein", "Samer Lone", "Michael K. Swan", "Jayati R. Choudhury", "Robert E. Johnson", "Satya Prakash", "Louise Prakash", "Aneel K. Aggarwal"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0005766.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Hoogsteen_base_pairing_between_8_oxoG_syn_and_incoming_dATP_/566487", "title"=>"Hoogsteen base pairing between 8-oxoG(<i>syn</i>) and incoming dATP.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:45:59"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/896156/Figure_3.tif"], "description"=>"<p>(A) Superimposition of the 8-oxoG complex (red) and the complex with undamaged DNA (blue; PDB code 2OH2). Highlighted are the template bases (8-oxoG and A), incoming dNTPs (dATP and dTTP) and residues within the active site cleft. A putative Mg<sup>2+</sup> ion is shown as a yellow sphere. (B) Superposition of template 8-oxoG(<i>syn)</i> (red) and template A(<i>anti</i>) (blue). The figure shows the stacking of the M135 side chain over the template bases, and the relative position of A151.</p>", "links"=>[], "tags"=>["undamaged"], "article_id"=>566610, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Rodrigo Vasquez-Del Carpio", "Timothy D. Silverstein", "Samer Lone", "Michael K. Swan", "Jayati R. Choudhury", "Robert E. Johnson", "Satya Prakash", "Louise Prakash", "Aneel K. Aggarwal"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0005766.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Damaged_versus_undamaged_DNA_/566610", "title"=>"Damaged versus undamaged DNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:46:38"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/896261/Figure_4.tif"], "description"=>"<p>Close up views of the Polκ (A) and Dpo4 (B) active site regions with template 8-oxoG. Highlighted and labeled are some of the residues implicated in stabilizing 8-oxoG (<i>syn</i>) in the Polκ active site region (M135 and A151) and 8-oxoG (<i>anti</i>) in the Dpo4 active site region (R331, R332 and S34). In the Polκ active site the putative Mg2<sup>+</sup> ion is shown as a yellow sphere. In the Dpo4 complex <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005766#pone.0005766-Rechkoblit1\" target=\"_blank\">[26]</a>, a water mediated hydrogen bond between R332 and O8 of 8-oxoG in Dpo4 is highlighted. The blue and orange spheres represent the water molecule and the calcium ions respectively. (C) A Hoogsteen 8-oxoG(<i>syn</i>):dATP (<i>anti</i>) base pair in the Polκ structure. (D) A W-C 8-oxoG(<i>anti</i>):dCTP (<i>anti</i>) base pair in the Dpo4 structure.</p>", "links"=>[], "tags"=>["dpo4"], "article_id"=>566713, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Rodrigo Vasquez-Del Carpio", "Timothy D. Silverstein", "Samer Lone", "Michael K. Swan", "Jayati R. Choudhury", "Robert E. Johnson", "Satya Prakash", "Louise Prakash", "Aneel K. Aggarwal"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0005766.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Comparison_between_Pol_954_and_Dpo4_active_site_regions_/566713", "title"=>"Comparison between Polκ and Dpo4 active site regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:47:14"}

PMC Usage Stats | Further Information

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