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==Crystal structure of Arabidopsis thaliana FPG==
==Crystal structure of Arabidopsis thaliana FPG==
<StructureSection load='3twm' size='340' side='right' caption='[[3twm]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='3twm' size='340' side='right'caption='[[3twm]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3twm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TWM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TWM FirstGlance]. <br>
<table><tr><td colspan='2'>[[3twm]] is a 6 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=3TWM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TWM FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3twk|3twk]], [[3twl|3twl]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fpg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=3twm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twm OCA], [https://pdbe.org/3twm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3twm RCSB], [https://www.ebi.ac.uk/pdbsum/3twm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3twm ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3twm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3twm RCSB], [http://www.ebi.ac.uk/pdbsum/3twm PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/Q9SBB4_ARATH Q9SBB4_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:9819050</ref> <ref>PMID:11272725</ref> <ref>PMID:22789755</ref>
[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[DNA glycosylase|DNA glycosylase]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: DNA-formamidopyrimidine glycosylase]]
[[Category: Large Structures]]
[[Category: Aller, P]]
[[Category: Aller P]]
[[Category: Doublie, S]]
[[Category: Doublie S]]
[[Category: Duclos, S]]
[[Category: Duclos S]]
[[Category: Wallace, S S]]
[[Category: Wallace SS]]
[[Category: Dna containing stable analog of abasic site]]
[[Category: Dna damage]]
[[Category: Dna repair]]
[[Category: Dna-binding]]
[[Category: Glycosidase]]
[[Category: Helix two turns helix]]
[[Category: Hydrolase]]
[[Category: Hydrolase-dna complex]]
[[Category: Lyase]]
[[Category: Multifunctional enzyme]]
[[Category: Tetrahydro furan]]
[[Category: Zinc-less finger]]

Latest revision as of 16:41, 14 March 2024

Crystal structure of Arabidopsis thaliana FPGCrystal structure of Arabidopsis thaliana FPG

Structural highlights

3twm is a 6 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3]

See Also

References

  1. ↑ Gao MJ, Murphy TM. Alternative forms of formamidopyrimidine-DNA glycosylase from Arabidopsis thaliana. Photochem Photobiol. 2001 Feb;73(2):128-34. PMID:11272725
  2. ↑ Duclos S, Aller P, Jaruga P, Dizdaroglu M, Wallace SS, Doublie S. Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine. DNA Repair (Amst). 2012 Jul 10. PMID:22789755 doi:10.1016/j.dnarep.2012.06.004
  3. ↑ Ohtsubo T, Matsuda O, Iba K, Terashima I, Sekiguchi M, Nakabeppu Y. Molecular cloning of AtMMH, an Arabidopsis thaliana ortholog of the Escherichia coli mutM gene, and analysis of functional domains of its product. Mol Gen Genet. 1998 Oct;259(6):577-90. PMID:9819050

3twm, resolution 2.80Å

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