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3twl

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Current revision (13:41, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3twl' size='340' side='right'caption='[[3twl]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='3twl' size='340' side='right'caption='[[3twl]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3twl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TWL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3twl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TWL FirstGlance]. <br>
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</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></td></tr>
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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]] 1.7&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3twk|3twk]], [[3twm|3twm]]</div></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=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fpg1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </span></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=3twl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twl OCA], [https://pdbe.org/3twl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3twl RCSB], [https://www.ebi.ac.uk/pdbsum/3twl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3twl ProSAT]</span></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=3twl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twl OCA], [https://pdbe.org/3twl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3twl RCSB], [https://www.ebi.ac.uk/pdbsum/3twl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3twl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/FPG_ARATH FPG_ARATH]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Can process efficiently 4,6-diamino-5-formamidopyrimidine (FapyA), 2,6-diamino-4- hydroxy-5-formamidopyrimidine (FapyG) and the further oxidation products of 8-oxoguanine (8-oxoG), such as guanidinohydantoin and spiroiminodihydantoin. Has marginal activity towards 8-oxoG. Has AP (apurinic/apyrimidinic) lyase activity. 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:11272725</ref> <ref>PMID:22789755</ref> <ref>PMID:9819050</ref>
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[https://www.uniprot.org/uniprot/FPG_ARATH FPG_ARATH] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Can process efficiently 4,6-diamino-5-formamidopyrimidine (FapyA), 2,6-diamino-4- hydroxy-5-formamidopyrimidine (FapyG) and the further oxidation products of 8-oxoguanine (8-oxoG), such as guanidinohydantoin and spiroiminodihydantoin. Has marginal activity towards 8-oxoG. Has AP (apurinic/apyrimidinic) lyase activity. 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:11272725</ref> <ref>PMID:22789755</ref> <ref>PMID:9819050</ref>
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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; MutM) is a DNA repair enzyme widely distributed in bacteria. Fpg recognizes and excises oxidatively modified purines, 4,6-diamino-5-formamidopyrimidine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine and 8-oxoguanine (8-oxoG), with similar excision kinetics. It exhibits some lesser activity toward 8-oxoadenine. Fpg enzymes are also present in some plant and fungal species. The eukaryotic Fpg homologs exhibit little or no activity on DNA containing 8-oxoG, but they recognize and process its oxidation products, guanidinohydantoin (Gh) and spiroiminohydantoin (Sp). To date, several structures of bacterial Fpg enzymes unliganded or in complex with DNA containing a damaged base have been published but there is no structure of a eukaryotic Fpg. Here we describe the first crystal structure of a plant Fpg, Arabidopsis thaliana (AthFpg), unliganded and bound to DNA containing an abasic site analog, tetrahydrofuran (THF). Although AthFpg shares a common architecture with other Fpg glycosylases, it harbors a zincless finger, previously described in a subset of Nei enzymes, such as human NEIL1 and Mimivirus Nei1. Importantly the "alphaF-beta9/10 loop" capping 8-oxoG in the active site of bacterial Fpg is very short in AthFpg. Deletion of a segment encompassing residues 213-229 in Escherichia coli Fpg (EcoFpg) and corresponding to the "alphaF-beta9/10 loop" does not affect the recognition and removal of oxidatively damaged DNA base lesions, with the exception of 8-oxoG. Although the exact role of the loop remains to be further explored, it is now clear that this protein segment is specific to the processing of 8-oxoG.
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Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine.,Duclos S, Aller P, Jaruga P, Dizdaroglu M, Wallace SS, Doublie S DNA Repair (Amst). 2012 Jul 10. PMID:22789755<ref>PMID:22789755</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3twl" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Arath]]
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[[Category: Arabidopsis thaliana]]
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[[Category: DNA-formamidopyrimidine glycosylase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Aller, P]]
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[[Category: Aller P]]
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[[Category: Doublie, S]]
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[[Category: Doublie S]]
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[[Category: Duclos, S]]
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[[Category: Duclos S]]
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[[Category: Wallace, S S]]
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[[Category: Wallace SS]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Dna-binding]]
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[[Category: Glycosidase]]
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[[Category: Helix two turns helix]]
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[[Category: Hydrolase]]
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[[Category: Lyase]]
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[[Category: Multifunctional enzyme]]
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[[Category: Zinc-less finger]]
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Current revision

Crystal structure of Arabidopsis thaliana FPG

PDB ID 3twl

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