1kfv

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{{Seed}}
 
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[[Image:1kfv.png|left|200px]]
 
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==Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.==
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The line below this paragraph, containing "STRUCTURE_1kfv", creates the "Structure Box" on the page.
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<StructureSection load='1kfv' size='340' side='right'caption='[[1kfv]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1kfv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KFV FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.55&#8491;</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PDI:PHOSPHORIC+ACID+MONO-(3-HYDROXY-PROPYL)+ESTER'>PDI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1kfv| PDB=1kfv | SCENE= }}
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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=1kfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kfv OCA], [https://pdbe.org/1kfv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kfv RCSB], [https://www.ebi.ac.uk/pdbsum/1kfv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kfv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/FPG_LACLC FPG_LACLC] 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). 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.<ref>PMID:7704272</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kf/1kfv_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</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/main_output.php?pdb_ID=1kfv ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The formamidopyrimidine-DNA glycosylase (Fpg, MutM) is a bifunctional base excision repair enzyme (DNA glycosylase/AP lyase) that removes a wide range of oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from oxidatively damaged DNA. The structure of a non-covalent complex between the Lactoccocus lactis Fpg and a 1,3-propanediol (Pr) abasic site analogue-containing DNA has been solved. Through an asymmetric interaction along the damaged strand and the intercalation of the triad (M75/R109/F111), Fpg pushes out the Pr site from the DNA double helix, recognizing the cytosine opposite the lesion and inducing a 60 degrees bend of the DNA. The specific recognition of this cytosine provides some structural basis for understanding the divergence between Fpg and its structural homologue endo nuclease VIII towards their substrate specificities. In addition, the modelling of the 8-oxoguanine residue allows us to define an enzyme pocket that may accommodate the extrahelical oxidized base.
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===Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.===
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Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.,Serre L, Pereira de Jesus K, Boiteux S, Zelwer C, Castaing B EMBO J. 2002 Jun 17;21(12):2854-65. PMID:12065399<ref>PMID:12065399</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 1kfv" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12065399}}, adds the Publication Abstract to the page
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 12065399 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12065399}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1KFV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KFV OCA].
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==Reference==
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Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA., Serre L, Pereira de Jesus K, Boiteux S, Zelwer C, Castaing B, EMBO J. 2002 Jun 17;21(12):2854-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12065399 12065399]
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[[Category: DNA-formamidopyrimidine glycosylase]]
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[[Category: Lactococcus lactis]]
[[Category: Lactococcus lactis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Boiteux, S.]]
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[[Category: Boiteux S]]
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[[Category: Castaing, B.]]
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[[Category: Castaing B]]
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[[Category: Jesus, K Pereira de.]]
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[[Category: Pereira de Jesus K]]
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[[Category: Serre, L.]]
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[[Category: Serre L]]
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[[Category: Zelwer, C.]]
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[[Category: Zelwer C]]
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[[Category: Abasic site]]
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[[Category: Ap lyase]]
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[[Category: Dna]]
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[[Category: Dna repair enzyme]]
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[[Category: N-glycosylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 10:17:04 2008''
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Current revision

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.

PDB ID 1kfv

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