2van

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[[Image:2van.png|left|200px]]
 
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==Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses==
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The line below this paragraph, containing "STRUCTURE_2van", creates the "Structure Box" on the page.
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<StructureSection load='2van' size='340' side='right'caption='[[2van]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2van]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VAN 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]] 2.1&#8491;</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=2van FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2van OCA], [https://pdbe.org/2van PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2van RCSB], [https://www.ebi.ac.uk/pdbsum/2van PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2van ProSAT]</span></td></tr>
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{{STRUCTURE_2van| PDB=2van | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
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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/va/2van_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=2van ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Understanding how DNA polymerases control fidelity requires elucidation of the mechanisms of matched and mismatched dNTP incorporations. Little is known about the latter because mismatched complexes do not crystallize readily. In this report, we employed small-angle X-ray scattering (SAXS) and structural modeling to probe the conformations of different intermediate states of mammalian DNA polymerase beta (Pol beta) in its wild-type and an error-prone variant, I260Q. Our structural results indicate that the mismatched ternary complex lies in-between the open and the closed forms, but more closely resembles the open form for WT and the closed form for I260Q. On the basis of molecular modeling, this over-stabilization of mismatched ternary complex of I260Q is likely caused by formation of a hydrogen bonding network between the side chains of Gln(260), Tyr(296), Glu(295) and Arg(258), freeing up Asp(192) to coordinate MgdNTP. These results argue against recent reports suggesting that mismatched dNTP incorporations follow a conformational path distinctly different from that of matched dNTP incorporation, or that its conformational closing is a major contributor to fidelity.
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===NUCLEOTIDYL TRANSFER MECHANISM OF MISMATCHED DNTP INCORPORATION BY DNA POLYMERASE B BY STRUCTURAL AND KINETIC ANALYSES===
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Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.,Tang KH, Niebuhr M, Tung CS, Chan HC, Chou CC, Tsai MD Nucleic Acids Res. 2008 May;36(9):2948-57. Epub 2008 Apr 2. PMID:18385153<ref>PMID:18385153</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18385153}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2van" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18385153 is the PubMed ID number.
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{{ABSTRACT_PUBMED_18385153}}
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==About this Structure==
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[[2van]] is a 1 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAN OCA].
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==See Also==
==See Also==
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*[[DNA polymerase]]
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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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<ref group="xtra">PMID:18385153</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Chan, H.]]
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[[Category: Chan H]]
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[[Category: Chou, C.]]
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[[Category: Chou C]]
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[[Category: Niebuhr, M.]]
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[[Category: Niebuhr M]]
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[[Category: Tang, K.]]
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[[Category: Tang K]]
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[[Category: Tsai, M.]]
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[[Category: Tsai M]]
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[[Category: Tung, C.]]
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[[Category: Tung C]]

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Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses

PDB ID 2van

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