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1pjj

From Proteopedia

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Complex between the Lactococcus lactis Fpg and an abasic site containing DNA.

Structural highlights

1pjj is a 3 chain structure with sequence from Lactococcus lactis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3' and 5' sides by betadelta-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5'-C4'-C3' diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4' leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside.

Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA.,Pereira de Jesus K, Serre L, Zelwer C, Castaing B Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:16243784^[2]

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

References

↑ Duwat P, de Oliveira R, Ehrlich SD, Boiteux S. Repair of oxidative DNA damage in gram-positive bacteria: the Lactococcus lactis Fpg protein. Microbiology. 1995 Feb;141 ( Pt 2):411-7. PMID:7704272
↑ Pereira de Jesus K, Serre L, Zelwer C, Castaing B. Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA. Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:16243784 doi:http://dx.doi.org/33/18/5936

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pjj"

@@ Line 3: / Line 3: @@
 <StructureSection load='1pjj' size='340' side='right'caption='[[1pjj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pjj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_lactis"_lister_1873 "bacterium lactis" lister 1873]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PJJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PJJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pjj]] is a 3 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=1PJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PJJ FirstGlance]. <br>
-</td></tr><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=ZN:ZINC+ION'>ZN</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]] 1.9&#8491;</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>
+<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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kfv|1kfv]], [[1ee8|1ee8]], [[1k82|1k82]], [[1l1t|1l1t]]</div></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=1pjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pjj OCA], [https://pdbe.org/1pjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pjj RCSB], [https://www.ebi.ac.uk/pdbsum/1pjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pjj ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MUTM OR FPG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1358 "Bacterium lactis" Lister 1873])</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://proteopedia.org/fgij/fg.htm?mol=1pjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pjj OCA], [http://pdbe.org/1pjj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pjj RCSB], [http://www.ebi.ac.uk/pdbsum/1pjj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pjj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 32: @@
 ==See Also==
 *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
-*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]
-*[[Fpg Nei Protein Family|Fpg Nei Protein Family]]
-*[[Fpg Nei Protein Superfamily|Fpg Nei Protein Superfamily]]
-*[[User:Ramiro Barrantes/FpgNeiRepair|User:Ramiro Barrantes/FpgNeiRepair]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacterium lactis lister 1873]]
+[[Category: Lactococcus lactis]]
-[[Category: DNA-formamidopyrimidine glycosylase]]
 [[Category: Large Structures]]
-[[Category: Boiteux, S]]
+[[Category: Boiteux S]]
-[[Category: Castaing, B]]
+[[Category: Castaing B]]
-[[Category: Jesus, K Pereira de]]
+[[Category: Pereira de Jesus K]]
-[[Category: Serre, L]]
+[[Category: Serre L]]
-[[Category: Zelwer, C]]
+[[Category: Zelwer C]]
-[[Category: Abasic site]]
-[[Category: Dna repair]]
-[[Category: Fpg]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Mutm]]

1pjj

From Proteopedia

Current revision

Complex between the Lactococcus lactis Fpg and an abasic site containing DNA.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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