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1tdz

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(New page: 200px<br /><applet load="1tdz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tdz, resolution 1.80&Aring;" /> '''Crystal Structure Co...)
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[[Image:1tdz.gif|left|200px]]<br /><applet load="1tdz" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1tdz, resolution 1.80&Aring;" />
 
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'''Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA'''<br />
 
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==Overview==
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==Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA==
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Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that, excises oxidized purines such as 7,8-dihydro-8-oxoguanine (8-oxoG) and, 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) from damaged DNA., Here, we report the crystal structure of the Fpg protein from Lactococcus, lactis (LlFpg) bound to a carbocyclic FapydG (cFapydG)-containing DNA. The, structure reveals that Fpg stabilizes the cFapydG nucleoside into an, extrahelical conformation inside its substrate binding pocket. In contrast, to the recognition of the 8-oxodG lesion, which is bound with the, glycosidic bond in a syn conformation, the cFapydG lesion displays in the, complex an anti conformation. Furthermore, Fpg establishes interactions, with all the functional groups of the FapyG base lesion, which can be, classified in two categories: (i) those specifying a purine-derived lesion, (here a guanine) involved in the Watson-Crick face recognition of the, lesion and probably contributing to an optimal orientation of the, pyrimidine ring moiety in the binding pocket and (ii) those specifying the, imidazole ring-opened moiety of FapyG and probably participating also in, the rotameric selection of the FapydG nucleobase. These interactions, involve strictly conserved Fpg residues and structural water molecules, mediated interactions. The significant differences between the Fpg, recognition modes of 8-oxodG and FapydG provide new insights into the Fpg, substrate specificity.
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<StructureSection load='1tdz' size='340' side='right'caption='[[1tdz]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1tdz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TDZ 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]] 1.8&#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=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1tdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tdz OCA], [https://pdbe.org/1tdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tdz RCSB], [https://www.ebi.ac.uk/pdbsum/1tdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tdz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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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/td/1tdz_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=1tdz 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 ==
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Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines such as 7,8-dihydro-8-oxoguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) from damaged DNA. Here, we report the crystal structure of the Fpg protein from Lactococcus lactis (LlFpg) bound to a carbocyclic FapydG (cFapydG)-containing DNA. The structure reveals that Fpg stabilizes the cFapydG nucleoside into an extrahelical conformation inside its substrate binding pocket. In contrast to the recognition of the 8-oxodG lesion, which is bound with the glycosidic bond in a syn conformation, the cFapydG lesion displays in the complex an anti conformation. Furthermore, Fpg establishes interactions with all the functional groups of the FapyG base lesion, which can be classified in two categories: (i) those specifying a purine-derived lesion (here a guanine) involved in the Watson-Crick face recognition of the lesion and probably contributing to an optimal orientation of the pyrimidine ring moiety in the binding pocket and (ii) those specifying the imidazole ring-opened moiety of FapyG and probably participating also in the rotameric selection of the FapydG nucleobase. These interactions involve strictly conserved Fpg residues and structural water molecules mediated interactions. The significant differences between the Fpg recognition modes of 8-oxodG and FapydG provide new insights into the Fpg substrate specificity.
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==About this Structure==
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Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase.,Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B J Biol Chem. 2004 Oct 15;279(42):44074-83. Epub 2004 Jul 10. PMID:15249553<ref>PMID:15249553</ref>
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1TDZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis] with ZN and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TDZ 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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Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase., Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B, J Biol Chem. 2004 Oct 15;279(42):44074-83. Epub 2004 Jul 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15249553 15249553]
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</div>
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[[Category: DNA-formamidopyrimidine glycosylase]]
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<div class="pdbe-citations 1tdz" style="background-color:#fffaf0;"></div>
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[[Category: Lactococcus lactis]]
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[[Category: Single protein]]
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[[Category: Boiteux, S.]]
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[[Category: Carell, T.]]
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[[Category: Castaing, B.]]
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[[Category: Coste, F.]]
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[[Category: Ober, M.]]
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[[Category: Zelwer, C.]]
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[[Category: GOL]]
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[[Category: ZN]]
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[[Category: dna repair; fpg; mutm; fapy g]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:11:34 2007''
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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: Lactococcus lactis]]
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[[Category: Large Structures]]
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[[Category: Boiteux S]]
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[[Category: Carell T]]
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[[Category: Castaing B]]
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[[Category: Coste F]]
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[[Category: Ober M]]
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[[Category: Zelwer C]]

Current revision

Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA

PDB ID 1tdz

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