2f5o
From Proteopedia
(Difference between revisions)
(New page: 200px<br /><applet load="2f5o" size="350" color="white" frame="true" align="right" spinBox="true" caption="2f5o, resolution 2.05Å" /> '''MutM crosslinked to ...) |
|||
| (16 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:2f5o.gif|left|200px]]<br /><applet load="2f5o" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2f5o, resolution 2.05Å" /> | ||
| - | '''MutM crosslinked to undamaged DNA sampling G:C base pair IC3'''<br /> | ||
| - | == | + | ==MutM crosslinked to undamaged DNA sampling G:C base pair IC3== |
| - | DNA glycosylases must interrogate millions of base pairs of undamaged DNA | + | <StructureSection load='2f5o' size='340' side='right'caption='[[2f5o]], [[Resolution|resolution]] 2.05Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2f5o]] 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=2F5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5O 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]] 2.05Å</td></tr> | ||
| + | <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> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5o OCA], [https://pdbe.org/2f5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5o RCSB], [https://www.ebi.ac.uk/pdbsum/2f5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5o 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/f5/2f5o_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=2f5o 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. | ||
| - | + | 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> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2f5o" style="background-color:#fffaf0;"></div> | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ==See Also== | |
| + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Geobacillus stearothermophilus]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Banerjee A]] | ||
| + | [[Category: Santos WL]] | ||
| + | [[Category: Verdine GL]] | ||
Current revision
MutM crosslinked to undamaged DNA sampling G:C base pair IC3
| |||||||||||
