1huz

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(New page: 200px<br /><applet load="1huz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1huz, resolution 2.6&Aring;" /> '''CRYSTAL STRUCTURE OF ...)
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[[Image:1huz.gif|left|200px]]<br /><applet load="1huz" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1huz, resolution 2.6&Aring;" />
 
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'''CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP==
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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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<StructureSection load='1huz' size='340' side='right'caption='[[1huz]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1huz]] is a 6 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=1HUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HUZ 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]] 2.6&#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=MDN:METHYLENEDIPHOSPHONIC+ACID'>MDN</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=1huz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1huz OCA], [https://pdbe.org/1huz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1huz RCSB], [https://www.ebi.ac.uk/pdbsum/1huz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1huz 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/1huz_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=1huz 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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1HUZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with CR and MDN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Transferase Transferase], 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=1HUZ OCA].
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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*[[Z-DNA|Z-DNA]]
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==Reference==
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__TOC__
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11330999 11330999]
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</StructureSection>
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[[Category: Large Structures]]
[[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: CR]]
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[[Category: MDN]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:50:38 2007''
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CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP

PDB ID 1huz

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