1k3w

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{{Seed}}
 
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[[Image:1k3w.png|left|200px]]
 
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==Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA==
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The line below this paragraph, containing "STRUCTURE_1k3w", creates the "Structure Box" on the page.
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<StructureSection load='1k3w' size='340' side='right'caption='[[1k3w]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1k3w]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K3W FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.42&#8491;</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=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1k3w| PDB=1k3w | SCENE= }}
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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=1k3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3w OCA], [https://pdbe.org/1k3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k3w RCSB], [https://www.ebi.ac.uk/pdbsum/1k3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3w ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/END8_ECOLI END8_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 pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Acts on DNA bubble and 3'-fork structures, suggesting a role in replication-associated DNA repair. 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:20031487</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k3/1k3w_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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/main_output.php?pdb_ID=1k3w ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. However, Nei differs significantly from Fpg in substrate specificity. We determined the structure of Nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 A resolution. The crosslink is derived from a Schiff base intermediate that precedes beta-elimination and is stabilized by reduction with NaBH(4). Nei consists of two domains connected by a hinge region, creating a DNA binding cleft between domains. DNA in the complex is sharply kinked, the deoxyribitol moiety is bound covalently to Pro1 and everted from the duplex into the active site. Amino acids involved in substrate binding and catalysis are identified. Molecular modeling and analysis of amino acid conservation suggest a site for recognition of the damaged base. Based on structural features of the complex and site-directed mutagenesis studies, we propose a catalytic mechanism for Nei.
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===Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA===
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Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.,Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G EMBO J. 2002 Feb 15;21(4):789-800. PMID:11847126<ref>PMID:11847126</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1k3w" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_11847126}}, adds the Publication Abstract to the page
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 11847126 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_11847126}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1K3W is a 3 chains structure of sequences 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=1K3W OCA].
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==Reference==
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<ref group="xtra">PMID:11847126</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Fernandes, A S.]]
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[[Category: Large Structures]]
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[[Category: Gerchman, S E.]]
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[[Category: Fernandes AS]]
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[[Category: Gilboa, R.]]
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[[Category: Gerchman SE]]
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[[Category: Golan, G.]]
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[[Category: Gilboa R]]
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[[Category: Grollman, A P.]]
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[[Category: Golan G]]
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[[Category: Kycia, J H.]]
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[[Category: Grollman AP]]
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[[Category: Rieger, R A.]]
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[[Category: Kycia JH]]
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[[Category: Shoham, G.]]
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[[Category: Rieger RA]]
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[[Category: Zharkov, D O.]]
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[[Category: Shoham G]]
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[[Category: Hydrolase/dna]]
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[[Category: Zharkov DO]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:57:28 2009''
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Current revision

Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA

PDB ID 1k3w

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