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2f5q

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[[Image:2f5q.gif|left|200px]]<br /><applet load="2f5q" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2f5q, resolution 2.35&Aring;" />
 
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'''Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC2'''<br />
 
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==Overview==
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==Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC2==
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<StructureSection load='2f5q' size='340' side='right'caption='[[2f5q]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2f5q]] 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=2F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5Q 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]] 2.35&#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=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</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=2f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5q OCA], [https://pdbe.org/2f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5q RCSB], [https://www.ebi.ac.uk/pdbsum/2f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5q 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/f5/2f5q_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=2f5q 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 ==
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.
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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2F5Q 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> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=2F5Q 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 2f5q" 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: ZN]]
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[[Category: control complex]]
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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 Thu Feb 21 17:17:57 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

Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC2

PDB ID 2f5q

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