1bnk

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[[Image:1bnk.gif|left|200px]]
 
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{{Structure
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==HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA==
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|PDB= 1bnk |SIZE=350|CAPTION= <scene name='initialview01'>1bnk</scene>, resolution 2.7&Aring;
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<StructureSection load='1bnk' size='340' side='right'caption='[[1bnk]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=YRR:3-HYDROXY-PYRROLIDIN-2-YLMETHYL-MONOPHOSPHATE+GROUP'>YRR</scene>
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<table><tr><td colspan='2'>[[1bnk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BNK FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] </span>
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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]] 2.7&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YRR:3-HYDROXY-PYRROLIDIN-2-YLMETHYL-MONOPHOSPHATE+GROUP'>YRR</scene></td></tr>
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|DOMAIN=
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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=1bnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bnk OCA], [https://pdbe.org/1bnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bnk RCSB], [https://www.ebi.ac.uk/pdbsum/1bnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bnk ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bnk OCA], [http://www.ebi.ac.uk/pdbsum/1bnk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bnk RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/3MG_HUMAN 3MG_HUMAN] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine, and 7-methylguanine from the damaged DNA polymer formed by alkylation lesions.
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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/bn/1bnk_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=1bnk 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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DNA N-glycosylases are base excision-repair proteins that locate and cleave damaged bases from DNA as the first step in restoring the genetic blueprint. The human enzyme 3-methyladenine DNA glycosylase removes a diverse group of damaged bases from DNA, including cytotoxic and mutagenic alkylation adducts of purines. We report the crystal structure of human 3-methyladenine DNA glycosylase complexed to a mechanism-based pyrrolidine inhibitor. The enzyme has intercalated into the minor groove of DNA, causing the abasic pyrrolidine nucleotide to flip into the enzyme active site, where a bound water is poised for nucleophilic attack. The structure shows an elegant means of exposing a nucleotide for base excision as well as a network of residues that could catalyze the in-line displacement of a damaged base from the phosphodeoxyribose backbone.
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'''HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA'''
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Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.,Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T Cell. 1998 Oct 16;95(2):249-58. PMID:9790531<ref>PMID:9790531</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 1bnk" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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DNA N-glycosylases are base excision-repair proteins that locate and cleave damaged bases from DNA as the first step in restoring the genetic blueprint. The human enzyme 3-methyladenine DNA glycosylase removes a diverse group of damaged bases from DNA, including cytotoxic and mutagenic alkylation adducts of purines. We report the crystal structure of human 3-methyladenine DNA glycosylase complexed to a mechanism-based pyrrolidine inhibitor. The enzyme has intercalated into the minor groove of DNA, causing the abasic pyrrolidine nucleotide to flip into the enzyme active site, where a bound water is poised for nucleophilic attack. The structure shows an elegant means of exposing a nucleotide for base excision as well as a network of residues that could catalyze the in-line displacement of a damaged base from the phosphodeoxyribose backbone.
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1BNK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNK OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision., Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T, Cell. 1998 Oct 16;95(2):249-58. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9790531 9790531]
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[[Category: DNA-3-methyladenine glycosylase II]]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Ellenberger, T.]]
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[[Category: Ellenberger T]]
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[[Category: Lau, A Y.]]
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[[Category: Lau AY]]
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[[Category: Samson, L.]]
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[[Category: Samson L]]
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[[Category: Schaerer, O D.]]
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[[Category: Schaerer OD]]
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[[Category: Verdine, G L.]]
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[[Category: Verdine GL]]
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[[Category: dna glycosylase]]
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[[Category: dna repair]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:04:34 2008''
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Current revision

HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA

PDB ID 1bnk

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