3c58
From Proteopedia
(Difference between revisions)
| (5 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:3c58.png|left|200px]] | ||
| - | + | ==Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA== | |
| + | <StructureSection load='3c58' size='340' side='right'caption='[[3c58]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3c58]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris_MG1363 Lactococcus lactis subsp. cremoris MG1363]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C58 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]] 1.9Å</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=SOS:[(1R,2S,4R)-4-({2-AMINO-5-[BENZYL(FORMYL)AMINO]-6-OXO-1,6-DIHYDROPYRIMIDIN-4-YL}AMINO)-2-HYDROXYCYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>SOS</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=3c58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c58 OCA], [https://pdbe.org/3c58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c58 RCSB], [https://www.ebi.ac.uk/pdbsum/3c58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c58 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/FPG_LACLC FPG_LACLC] 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.<ref>PMID:7704272</ref> | ||
| + | == 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/c5/3c58_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=3c58 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Fpg is a bacterial base excision repair enzyme that removes oxidized purines from DNA. This work shows that Fpg and its eukaryote homolog Ogg1 recognize with high affinity FapydG and bulky N7-benzyl-FapydG (Bz-FapydG). The comparative crystal structure analysis of stable complexes between Fpg and carbocyclic cFapydG or Bz-cFapydG nucleoside-containing DNA provides the molecular basis of the ability of Fpg to bind both lesions with the same affinity and to differently process them. To accommodate the steric hindrance of the benzyl group, Fpg selects the adequate rotamer of the extrahelical Bz-cFapydG formamido group, forcing the bulky group to go outside the binding pocket. Contrary to the binding mode of cFapydG, the particular recognition of Bz-cFapydG leads the BER enzymes to unproductive complexes which would hide the lesion and slow down its repair by the NER machinery. | ||
| - | + | Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode.,Coste F, Ober M, Le Bihan YV, Izquierdo MA, Hervouet N, Mueller H, Carell T, Castaing B Chem Biol. 2008 Jul 21;15(7):706-17. PMID:18635007<ref>PMID:18635007</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 3c58" style="background-color:#fffaf0;"></div> | |
| - | + | ||
==See Also== | ==See Also== | ||
| - | *[[DNA | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| - | + | == References == | |
| - | == | + | <references/> |
| - | < | + | __TOC__ |
| - | [[Category: Lactococcus lactis | + | </StructureSection> |
| - | + | [[Category: Lactococcus lactis subsp. cremoris MG1363]] | |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Carell T]] |
| - | [[Category: | + | [[Category: Castaing B]] |
| - | [[Category: | + | [[Category: Coste F]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA
| |||||||||||
