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2xzf

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Revision as of 12:28, 22 July 2020

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 293K

Structural highlights

2xzf is a 3 chain structure with sequence from "streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	1pji, 1pm5, 1xc8, 1tdz, 1pjj, 1kfv, 1nnj
Activity:	DNA-formamidopyrimidine glycosylase, with EC number 3.2.2.23
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]

Publication Abstract from PubMed

DNA base-damage recognition in the base excision repair (BER) is a process operating on a wide variety of alkylated, oxidized and degraded bases. DNA glycosylases are the key enzymes which initiate the BER pathway by recognizing and excising the base damages guiding the damaged DNA through repair synthesis. We report here biochemical and structural evidence for the irreversible entrapment of DNA glycosylases by 5-hydroxy-5-methylhydantoin, an oxidized thymine lesion. The first crystal structure of a suicide complex between DNA glycosylase and unrepaired DNA has been solved. In this structure, the formamidopyrimidine-(Fapy) DNA glycosylase from Lactococcus lactis (LlFpg/LlMutM) is covalently bound to the hydantoin carbanucleoside-containing DNA. Coupling a structural approach by solving also the crystal structure of the non-covalent complex with site directed mutagenesis, this atypical suicide reaction mechanism was elucidated. It results from the nucleophilic attack of the catalytic N-terminal proline of LlFpg on the C5-carbon of the base moiety of the hydantoin lesion. The biological significance of this finding is discussed.

5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases.,Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B Nucleic Acids Res. 2011 Aug;39(14):6277-90. Epub 2011 Apr 12. PMID:21486746^[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
↑ Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B. 5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases. Nucleic Acids Res. 2011 Aug;39(14):6277-90. Epub 2011 Apr 12. PMID:21486746 doi:10.1093/nar/gkr215

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/2xzf"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 293K==
-<StructureSection load='2xzf' size='340' side='right' caption='[[2xzf]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='2xzf' size='340' side='right'caption='[[2xzf]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xzf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XZF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xzf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XZF 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=VET:[(1R,2S,4R)-2-HYDROXY-4-[(5R)-5-HYDROXY-5-METHYL-2,4-DIOXO-IMIDAZOLIDIN-1-YL]CYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>VET</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pji|1pji]], [[1pm5|1pm5]], [[1xc8|1xc8]], [[1tdz|1tdz]], [[1pjj|1pjj]], [[1kfv|1kfv]], [[1nnj|1nnj]]</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=2xzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzf OCA], [http://pdbe.org/2xzf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xzf RCSB], [http://www.ebi.ac.uk/pdbsum/2xzf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzf ProSAT]</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=2xzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzf OCA], [http://pdbe.org/2xzf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xzf RCSB], [http://www.ebi.ac.uk/pdbsum/2xzf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzf ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 23: @@
 ==See Also==
-*[[DNA glycosylase|DNA glycosylase]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 == References ==
 <references/>
@@ Line 30: / Line 30: @@
 [[Category: Streptococcus hollandicus scholl 1891]]
 [[Category: DNA-formamidopyrimidine glycosylase]]
+[[Category: Large Structures]]
 [[Category: Aller, P]]
 [[Category: Carrel, T]]

2xzf

From Proteopedia

Revision as of 12:28, 22 July 2020

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 293K

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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