2f5s: Difference between revisions

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[[Image:2f5s.gif|left|200px]]
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{{STRUCTURE_2f5s|  PDB=2f5s  |  SCENE=  }}
'''Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC1'''


==Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC1==
<StructureSection load='2f5s' size='340' side='right'caption='[[2f5s]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2f5s]] 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=2F5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5S FirstGlance]. <br>
</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>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5s OCA], [https://pdbe.org/2f5s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5s RCSB], [https://www.ebi.ac.uk/pdbsum/2f5s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5s ProSAT]</span></td></tr>
</table>
== Function ==
[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]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/2f5s_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2f5s ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


==Overview==
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>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2F5S is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5S OCA].
</div>
<div class="pdbe-citations 2f5s" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structure of a DNA glycosylase searching for lesions., Banerjee A, Santos WL, Verdine GL, Science. 2006 Feb 24;311(5764):1153-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16497933 16497933]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
[[Category: DNA-formamidopyrimidine glycosylase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Banerjee, A.]]
[[Category: Banerjee A]]
[[Category: Santos, W L.]]
[[Category: Santos WL]]
[[Category: Verdine, G L.]]
[[Category: Verdine GL]]
[[Category: Control complex]]
[[Category: Damage search]]
[[Category: Disulfide crosslink]]
[[Category: Dna glycosylase]]
[[Category: Dna repair]]
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Retrieved from "https://proteopedia.org/2f5s"