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3twk

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Revision as of 07:58, 4 August 2016

Crystal structure of arabidopsis thaliana FPG

Structural highlights

3twk is a 2 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	3twl, 3twm
Gene:	fpg1 (ARATH)
Activity:	DNA-formamidopyrimidine glycosylase, with EC number 3.2.2.23
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]

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gao MJ, Murphy TM. Alternative forms of formamidopyrimidine-DNA glycosylase from Arabidopsis thaliana. Photochem Photobiol. 2001 Feb;73(2):128-34. PMID:11272725
↑ 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
↑ 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
↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3twk"

@@ Line 1: / Line 1: @@
 ==Crystal structure of arabidopsis thaliana FPG==
 <StructureSection load='3twk' size='340' side='right' caption='[[3twk]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3twk]] is a 2 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=3TWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TWK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3twk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TWK FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3twl|3twl]], [[3twm|3twm]]</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='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 ARATH])</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=3twk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3twk RCSB], [http://www.ebi.ac.uk/pdbsum/3twk PDBsum]</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=3twk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3twk OCA], [http://pdbe.org/3twk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3twk RCSB], [http://www.ebi.ac.uk/pdbsum/3twk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3twk ProSAT]</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>
+[[http://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 ==
@@ Line 20: / Line 21: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3twk" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 27: / Line 29: @@
 __TOC__
 </StructureSection>
-[[Category: Arabidopsis thaliana]]
+[[Category: Arath]]
 [[Category: DNA-formamidopyrimidine glycosylase]]
 [[Category: Aller, P]]

3twk

From Proteopedia

Revision as of 07:58, 4 August 2016

Crystal structure of arabidopsis thaliana FPG

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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