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2flp

From Proteopedia

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(New page: 200px<br /> <applet load="2flp" size="450" color="white" frame="true" align="right" spinBox="true" caption="2flp, resolution 2.40&Aring;" /> '''Binary complex of t...)
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[[Image:2flp.gif|left|200px]]<br />
 
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<applet load="2flp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2flp, resolution 2.40&Aring;" />
 
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'''Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)'''<br />
 
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==Overview==
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==Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)==
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Substrate-induced conformational change of the protein is the linchpin of, enzymatic reactions. Replicative DNA polymerases, for example, convert, from an open to a closed conformation in response to dNTP binding. Human, DNA polymerase-iota (hPoliota), a member of the Y family of DNA, polymerases, differs strikingly from other polymerases in its much higher, proficiency and fidelity for nucleotide incorporation opposite template, purines than opposite template pyrimidines. We present here a, crystallographic analysis of hPoliota binary complexes, which together, with the ternary complexes show that, contrary to replicative DNA, polymerases, the DNA, and not the polymerase, undergoes the primary, substrate-induced conformational change. The incoming dNTP "pushes", templates A and G from the anti to the syn conformation dictated by a, rigid hPoliota active site. Together, the structures posit a mechanism for, template selection wherein dNTP binding induces a conformational switch in, template purines for productive Hoogsteen base pairing.
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<StructureSection load='2flp' size='340' side='right'caption='[[2flp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2flp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FLP FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2flp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2flp OCA], [https://pdbe.org/2flp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2flp RCSB], [https://www.ebi.ac.uk/pdbsum/2flp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2flp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fl/2flp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2flp ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2FLP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FLP OCA].
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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==Reference==
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<references/>
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An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site., Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK, Structure. 2006 Apr;14(4):749-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16615915 16615915]
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__TOC__
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[[Category: DNA-directed DNA polymerase]]
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Aggarwal, A.K.]]
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[[Category: Aggarwal AK]]
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[[Category: Johnson, R.E.]]
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[[Category: Johnson RE]]
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[[Category: Nair, D.T.]]
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[[Category: Nair DT]]
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[[Category: Prakash, L.]]
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[[Category: Prakash L]]
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[[Category: Prakash, S.]]
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[[Category: Prakash S]]
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[[Category: binary complex]]
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[[Category: dna polymerase]]
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[[Category: lesion bypass]]
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[[Category: template g]]
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[[Category: y-family]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 22:07:10 2007''
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Current revision

Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)

PDB ID 2flp

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