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1k82

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==Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA==
==Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA==
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<StructureSection load='1k82' size='340' side='right' caption='[[1k82]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<StructureSection load='1k82' size='340' side='right'caption='[[1k82]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1k82]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K82 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K82 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1k82]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K82 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K82 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.1&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></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=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fpg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1k82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k82 OCA], [https://pdbe.org/1k82 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k82 RCSB], [https://www.ebi.ac.uk/pdbsum/1k82 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k82 ProSAT]</span></td></tr>
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<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>
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<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=1k82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k82 OCA], [http://pdbe.org/1k82 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k82 RCSB], [http://www.ebi.ac.uk/pdbsum/1k82 PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/FPG_ECOLI FPG_ECOLI]] 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) and its derivatives such as guanidinohydantoin:C and spiroiminodihydantoin:C, however it also acts on thymine glycol:G, 5,6-dihydrouracil:G and 5-hydroxyuracil:G. 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. Cleaves ssDNA containing an AP site.<ref>PMID:1689309</ref> <ref>PMID:20031487</ref>
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[https://www.uniprot.org/uniprot/FPG_ECOLI FPG_ECOLI] 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) and its derivatives such as guanidinohydantoin:C and spiroiminodihydantoin:C, however it also acts on thymine glycol:G, 5,6-dihydrouracil:G and 5-hydroxyuracil:G. 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. Cleaves ssDNA containing an AP site.<ref>PMID:1689309</ref> <ref>PMID:20031487</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/1k82_consurf.spt"</scriptWhenChecked>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/1k82_consurf.spt"</scriptWhenChecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
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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=1k82 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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==See Also==
==See Also==
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*[[DNA glycosylase|DNA glycosylase]]
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]
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*[[Fpg Nei Protein Family|Fpg Nei Protein Family]]
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*[[Fpg Nei Protein Superfamily|Fpg Nei Protein Superfamily]]
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus coli migula 1895]]
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[[Category: Escherichia coli]]
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[[Category: DNA-formamidopyrimidine glycosylase]]
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[[Category: Large Structures]]
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[[Category: Fernandes, A S]]
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[[Category: Fernandes AS]]
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[[Category: Gerchman, S E]]
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[[Category: Gerchman SE]]
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[[Category: Gilboa, R]]
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[[Category: Gilboa R]]
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[[Category: Golan, G]]
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[[Category: Golan G]]
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[[Category: Grollman, A P]]
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[[Category: Grollman AP]]
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[[Category: Kycia, J H]]
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[[Category: Kycia JH]]
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[[Category: Matz, E]]
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[[Category: Matz E]]
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[[Category: Shoham, G]]
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[[Category: Shoham G]]
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[[Category: Zharkov, D O]]
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[[Category: Zharkov DO]]
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[[Category: Beta sandwich]]
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[[Category: Dna repair]]
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[[Category: Helix two-turns helix]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Protein-dna complex]]
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[[Category: Zinc finger]]
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Current revision

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

PDB ID 1k82

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