3twm: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==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 ==
-<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>
 == 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==
-*[[DNA glycosylase|DNA glycosylase]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 == References ==
 <references/>
@@ Line 27: / Line 18: @@
 </StructureSection>
 [[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]]