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1k3w

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[[Image:1k3w.gif|left|200px]]
 
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{{Structure
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==Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA==
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|PDB= 1k3w |SIZE=350|CAPTION= <scene name='initialview01'>1k3w</scene>, resolution 1.42&Aring;
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<StructureSection load='1k3w' size='340' side='right'caption='[[1k3w]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
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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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|ACTIVITY=
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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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|GENE= nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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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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}}
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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/initialview01.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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'''Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA'''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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==Overview==
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<references/>
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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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__TOC__
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</StructureSection>
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==About this Structure==
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1K3W is a [[Single protein]] structure of 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=1K3W OCA].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/11847126 11847126]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Fernandes, A S.]]
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[[Category: Fernandes AS]]
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[[Category: Gerchman, S E.]]
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[[Category: Gerchman SE]]
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[[Category: Gilboa, R.]]
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[[Category: Gilboa R]]
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[[Category: Golan, G.]]
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[[Category: Golan G]]
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[[Category: Grollman, A P.]]
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[[Category: Grollman AP]]
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[[Category: Kycia, J H.]]
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[[Category: Kycia JH]]
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[[Category: Rieger, R A.]]
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[[Category: Rieger RA]]
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[[Category: Shoham, G.]]
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[[Category: Shoham G]]
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[[Category: Zharkov, D O.]]
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[[Category: Zharkov DO]]
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[[Category: SO4]]
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[[Category: ZN]]
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[[Category: hydrolase/dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:12:13 2008''
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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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