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3c58

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Current revision (14:55, 1 November 2023) (edit) (undo)
 
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<StructureSection load='3c58' size='340' side='right'caption='[[3c58]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3c58' size='340' side='right'caption='[[3c58]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3c58]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Laclm Laclm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C58 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3c58]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris_MG1363 Lactococcus lactis subsp. cremoris MG1363]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C58 FirstGlance]. <br>
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</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>
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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]] 1.9&#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=SOS:[(1R,2S,4R)-4-({2-AMINO-5-[BENZYL(FORMYL)AMINO]-6-OXO-1,6-DIHYDROPYRIMIDIN-4-YL}AMINO)-2-HYDROXYCYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>SOS</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SOS:[(1R,2S,4R)-4-({2-AMINO-5-[BENZYL(FORMYL)AMINO]-6-OXO-1,6-DIHYDROPYRIMIDIN-4-YL}AMINO)-2-HYDROXYCYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>SOS</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">MUTM, FPG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=416870 LACLM])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></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=3c58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c58 OCA], [https://pdbe.org/3c58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c58 RCSB], [https://www.ebi.ac.uk/pdbsum/3c58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c58 ProSAT]</span></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=3c58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c58 OCA], [https://pdbe.org/3c58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c58 RCSB], [https://www.ebi.ac.uk/pdbsum/3c58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c58 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/A2RI84_LACLM A2RI84_LACLM]] 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 (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS015886_004_120556]
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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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Laclm]]
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[[Category: Lactococcus lactis subsp. cremoris MG1363]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Carell, T]]
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[[Category: Carell T]]
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[[Category: Castaing, B]]
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[[Category: Castaing B]]
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[[Category: Coste, F]]
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[[Category: Coste F]]
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[[Category: Benzyl-fapy]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Dna-binding]]
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[[Category: Glycosidase]]
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[[Category: Glycosylase]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Lyase]]
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[[Category: Metal-binding]]
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[[Category: Multifunctional enzyme]]
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[[Category: Protein-dna complex]]
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[[Category: Zinc-finger]]
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Current revision

Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA

PDB ID 3c58

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