1k82
From Proteopedia
(Difference between revisions)
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]] 2.10Å' scene=''> | |
- | + | == Structural highlights == | |
+ | <table><tr><td colspan='2'>[[1k82]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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> | ||
+ | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br> | ||
+ | <tr><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><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 Escherichia coli])</td></tr> | ||
+ | <tr><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><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://www.rcsb.org/pdb/explore.do?structureId=1k82 RCSB], [http://www.ebi.ac.uk/pdbsum/1k82 PDBsum]</span></td></tr> | ||
+ | <table> | ||
+ | == Evolutionary Conservation == | ||
+ | [[Image:Consurf_key_small.gif|200px|right]] | ||
+ | Check<jmol> | ||
+ | <jmolCheckbox> | ||
+ | <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> | ||
+ | </jmolCheckbox> | ||
+ | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | ||
+ | <div style="clear:both"></div> | ||
+ | <div style="background-color:#fffaf0;"> | ||
+ | == 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<ref>PMID:11912217</ref> | |
- | + | ||
+ | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
+ | </div> | ||
==See Also== | ==See Also== | ||
- | *[[DNA | + | *[[DNA glycosylase|DNA glycosylase]] |
*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]] | *[[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 Family|Fpg Nei Protein Family]] | ||
*[[Fpg Nei Protein Superfamily|Fpg Nei Protein Superfamily]] | *[[Fpg Nei Protein Superfamily|Fpg Nei Protein Superfamily]] | ||
- | + | == References == | |
- | == | + | <references/> |
- | < | + | __TOC__ |
+ | </StructureSection> | ||
[[Category: DNA-formamidopyrimidine glycosylase]] | [[Category: DNA-formamidopyrimidine glycosylase]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] |
Revision as of 11:54, 3 October 2014
Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA
|
Categories: DNA-formamidopyrimidine glycosylase | Escherichia coli | Fernandes, A S. | Gerchman, S E. | Gilboa, R. | Golan, G. | Grollman, A P. | Kycia, J H. | Matz, E. | Shoham, G. | Zharkov, D O. | Beta sandwich | Dna repair | Helix two-turns helix | Hydrolase-dna complex | Protein-dna complex | Zinc finger