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1huo

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[[Image:1huo.gif|left|200px]]
 
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==CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP==
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The line below this paragraph, containing "STRUCTURE_1huo", creates the "Structure Box" on the page.
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<StructureSection load='1huo' size='340' side='right'caption='[[1huo]], [[Resolution|resolution]] 2.60&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'>[[1huo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cf6 1cf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HUO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HUO FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.6&#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=CR:CHROMIUM+ION'>CR</scene>, <scene name='pdbligand=TTE:PHOSPHOMETHYL+PHOSPHONIC+ACID+DEOXYTHYMIDYLATE+ESTER'>TTE</scene></td></tr>
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{{STRUCTURE_1huo| PDB=1huo | SCENE= }}
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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=1huo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1huo OCA], [https://pdbe.org/1huo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1huo RCSB], [https://www.ebi.ac.uk/pdbsum/1huo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1huo ProSAT]</span></td></tr>
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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/hu/1huo_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=1huo ConSurf].
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<div style="clear:both"></div>
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'''CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP'''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The catalytic reaction mediated by DNA polymerases is known to require two Mg(II) ions, one associated with dNTP binding and the other involved in metal ion catalysis of the chemical step. Here we report a functional intermediate structure of a DNA polymerase with only one metal ion bound, the DNA polymerase beta-DNA template-primer-chromium(III).2'-deoxythymidine 5'-beta,gamma-methylenetriphosphate [Cr(III).dTMPPCP] complex, at 2.6 A resolution. The complex is distinct from the structures of other polymerase-DNA-ddNTP complexes in that the 3'-terminus of the primer has a free hydroxyl group. Hence, this structure represents a fully functional intermediate state. Support for this contention is provided by the observation of turnover in biochemical assays of crystallized protein as well as from the determination that soaking Pol beta crystals with Mn(II) ions leads to formation of the product complex, Pol beta-DNA-Cr(III).PCP, whose structure is also reported. An important feature of both structures is that the fingers subdomain is closed, similar to structures of other ternary complexes in which both metal ion sites are occupied. These results suggest that closing of the fingers subdomain is induced specifically by binding of the metal-dNTP complex prior to binding of the catalytic Mg(2+) ion. This has led us to reevaluate our previous evidence regarding the existence of a rate-limiting conformational change in Pol beta's reaction pathway. The results of stopped-flow studies suggest that there is no detectable rate-limiting conformational change step.
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[[Category: Large Structures]]
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==About this Structure==
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1HUO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cf6 1cf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HUO OCA].
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==Reference==
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Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes., Arndt JW, Gong W, Zhong X, Showalter AK, Liu J, Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK, Biochemistry. 2001 May 8;40(18):5368-75. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11330999 11330999]
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Arndt JW]]
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[[Category: Transferase]]
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[[Category: Chan MK]]
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[[Category: Arndt, J W.]]
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[[Category: Gong W]]
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[[Category: Chan, M K.]]
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[[Category: Lin Z]]
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[[Category: Gong, W.]]
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[[Category: Liu J]]
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[[Category: Lin, Z.]]
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[[Category: Paxson C]]
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[[Category: Liu, J.]]
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[[Category: Showalter AK]]
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[[Category: Paxson, C.]]
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[[Category: Tsai M-D]]
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[[Category: Showalter, A K.]]
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[[Category: Zhong X]]
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[[Category: Tsai, M D.]]
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[[Category: Zhong, X.]]
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[[Category: Protein-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 19:14:51 2008''
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Current revision

CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP

PDB ID 1huo

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