1k82

From Proteopedia

(Difference between revisions)

Revision as of 07:41, 25 November 2020

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

Structural highlights

1k82 is a 12 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	fpg ("Bacillus coli" Migula 1895)
Activity:	DNA-formamidopyrimidine glycosylase, with EC number 3.2.2.23
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2]

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

Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. The Schiff base intermediate formed during this reaction between Escherichia coli Fpg and DNA was trapped by reduction with sodium borohydride, and the structure of the resulting covalently cross-linked complex was determined at a 2.1-A resolution. Fpg is a bilobal protein with a wide, positively charged DNA-binding groove. It possesses a conserved zinc finger and a helix-two turn-helix motif that participate in DNA binding. The absolutely conserved residues Lys-56, His-70, Asn-168, and Arg-258 form hydrogen bonds to the phosphodiester backbone of DNA, which is sharply kinked at the lesion site. Residues Met-73, Arg-109, and Phe-110 are inserted into the DNA helix, filling the void created by nucleotide eversion. A deep hydrophobic pocket in the active site is positioned to accommodate an everted base. Structural analysis of the Fpg-DNA complex reveals essential features of damage recognition and the catalytic mechanism of Fpg.

Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.,Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G J Biol Chem. 2002 May 31;277(22):19811-6. Epub 2002 Mar 23. PMID:11912217^[3]

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

References

↑ Boiteux S, O'Connor TR, Lederer F, Gouyette A, Laval J. Homogeneous Escherichia coli FPG protein. A DNA glycosylase which excises imidazole ring-opened purines and nicks DNA at apurinic/apyrimidinic sites. J Biol Chem. 1990 Mar 5;265(7):3916-22. PMID:1689309
↑ Guo Y, Bandaru V, Jaruga P, Zhao X, Burrows CJ, Iwai S, Dizdaroglu M, Bond JP, Wallace SS. The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts. DNA Repair (Amst). 2010 Feb 4;9(2):177-90. doi: 10.1016/j.dnarep.2009.11.008., Epub 2009 Dec 23. PMID:20031487 doi:http://dx.doi.org/10.1016/j.dnarep.2009.11.008
↑ Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G. Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. J Biol Chem. 2002 May 31;277(22):19811-6. Epub 2002 Mar 23. PMID:11912217 doi:http://dx.doi.org/10.1074/jbc.M202058200

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/1k82"

@@ Line 1: / Line 1: @@
 ==Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA==
-<StructureSection load='1k82' size='340' side='right' caption='[[1k82]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='1k82' size='340' side='right'caption='[[1k82]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<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://proteopedia.org/fgij/fg.htm?mol=1K82 FirstGlance]. <br>
-</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>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
 <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>
 <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=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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k82 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=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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k82 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k8/1k82_consurf.spt"</scriptWhenChecked>
+    <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>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 ==See Also==
-*[[DNA glycosylase|DNA glycosylase]]
+*[[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/>
@@ Line 43: / Line 44: @@
 [[Category: Bacillus coli migula 1895]]
 [[Category: DNA-formamidopyrimidine glycosylase]]
+[[Category: Large Structures]]
 [[Category: Fernandes, A S]]
 [[Category: Gerchman, S E]]

1k82

From Proteopedia

Revision as of 07:41, 25 November 2020

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