2f5n

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(New page: 200px<br /><applet load="2f5n" size="350" color="white" frame="true" align="right" spinBox="true" caption="2f5n, resolution 2.00&Aring;" /> '''MutM crosslinked to ...)
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[[Image:2f5n.gif|left|200px]]<br /><applet load="2f5n" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2f5n, resolution 2.00&Aring;" />
 
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'''MutM crosslinked to undamaged DNA sampling A:T base pair IC1'''<br />
 
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==Overview==
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==MutM crosslinked to undamaged DNA sampling A:T base pair IC1==
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DNA glycosylases must interrogate millions of base pairs of undamaged DNA, in order to locate and then excise one damaged nucleobase. The nature of, this search process remains poorly understood. Here we report the use of, disulfide cross-linking (DXL) technology to obtain structures of a, bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These, structures, solved to 2.0 angstrom resolution, reveal the nature of the, search process: The protein inserts a probe residue into the helical stack, and severely buckles the target base pair, which remains intrahelical., MutM therefore actively interrogates the intact DNA helix while searching, for damage.
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<StructureSection load='2f5n' size='340' side='right'caption='[[2f5n]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2f5n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5N 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&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2f5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5n OCA], [https://pdbe.org/2f5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5n RCSB], [https://www.ebi.ac.uk/pdbsum/2f5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5n ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
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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/f5/2f5n_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=2f5n 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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DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.
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==About this Structure==
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Structure of a DNA glycosylase searching for lesions.,Banerjee A, Santos WL, Verdine GL Science. 2006 Feb 24;311(5764):1153-7. PMID:16497933<ref>PMID:16497933</ref>
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2F5N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5N OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure of a DNA glycosylase searching for lesions., Banerjee A, Santos WL, Verdine GL, Science. 2006 Feb 24;311(5764):1153-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16497933 16497933]
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</div>
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[[Category: DNA-formamidopyrimidine glycosylase]]
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<div class="pdbe-citations 2f5n" style="background-color:#fffaf0;"></div>
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[[Category: Geobacillus stearothermophilus]]
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[[Category: Single protein]]
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[[Category: Banerjee, A.]]
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[[Category: Santos, W.L.]]
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[[Category: Verdine, G.L.]]
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[[Category: GOL]]
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[[Category: ZN]]
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[[Category: damage search]]
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[[Category: disulfide crosslink]]
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[[Category: dna glycosylase]]
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[[Category: dna repair]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 19:28:02 2008''
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==See Also==
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Geobacillus stearothermophilus]]
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[[Category: Large Structures]]
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[[Category: Banerjee A]]
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[[Category: Santos WL]]
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[[Category: Verdine GL]]

Current revision

MutM crosslinked to undamaged DNA sampling A:T base pair IC1

PDB ID 2f5n

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