This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2f5p
From Proteopedia
(Difference between revisions)
| (16 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:2f5p.gif|left|200px]]<br /><applet load="2f5p" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2f5p, resolution 2.00Å" /> | ||
| - | '''MutM crosslinked to undamaged DNA sampling A:T base pair IC2'''<br /> | ||
| - | == | + | ==MutM crosslinked to undamaged DNA sampling A:T base pair IC2== |
| - | + | <StructureSection load='2f5p' size='340' side='right'caption='[[2f5p]], [[Resolution|resolution]] 2.00Å' scene=''> | |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2f5p]] 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=2F5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5P 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]] 2Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=2f5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5p OCA], [https://pdbe.org/2f5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5p RCSB], [https://www.ebi.ac.uk/pdbsum/2f5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5p 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/f5/2f5p_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=2f5p ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| - | == | + | ==See Also== |
| - | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] | |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | + | ||
| - | + | ||
[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Banerjee | + | [[Category: Banerjee A]] |
| - | [[Category: Santos | + | [[Category: Santos WL]] |
| - | [[Category: Verdine | + | [[Category: Verdine GL]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
MutM crosslinked to undamaged DNA sampling A:T base pair IC2
| |||||||||||
