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3bkz

From Proteopedia

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{{Seed}}
 
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[[Image:3bkz.png|left|200px]]
 
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<!--
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==X-ray structure of E coli AlkB crosslinked to dsDNA in the active site==
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The line below this paragraph, containing "STRUCTURE_3bkz", creates the "Structure Box" on the page.
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<StructureSection load='3bkz' size='340' side='right'caption='[[3bkz]], [[Resolution|resolution]] 1.65&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'>[[3bkz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BKZ FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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-->
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene></td></tr>
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{{STRUCTURE_3bkz| PDB=3bkz | SCENE= }}
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fd8|2fd8]], [[2qxq|2qxq]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alkB, aidD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [https://pdbe.org/3bkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [https://www.ebi.ac.uk/pdbsum/3bkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bkz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</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/bk/3bkz_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=3bkz 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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Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.
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===X-ray structure of E coli AlkB crosslinked to dsDNA in the active site===
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Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.,Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C Nature. 2008 Apr 24;452(7190):961-5. PMID:18432238<ref>PMID:18432238</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 3bkz" style="background-color:#fffaf0;"></div>
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<!--
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18432238}}, adds the Publication Abstract to the page
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18432238 is the PubMed ID number.
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== References ==
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-->
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<references/>
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{{ABSTRACT_PUBMED_18432238}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Ecoli]]
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3BKZ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BKZ OCA].
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[[Category: Large Structures]]
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[[Category: He, C]]
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==Reference==
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[[Category: Yang, C G]]
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Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA., Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C, Nature. 2008 Apr 24;452(7190):961-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18432238 18432238]
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[[Category: Yi, C]]
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[[Category: Escherichia coli k12]]
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[[Category: Protein complex]]
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[[Category: He, C.]]
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[[Category: Yang, C G.]]
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[[Category: Yi, C.]]
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[[Category: Alkylation repair]]
[[Category: Alkylation repair]]
[[Category: Cross-linking]]
[[Category: Cross-linking]]
[[Category: Dioxygenase]]
[[Category: Dioxygenase]]
[[Category: Dna repair]]
[[Category: Dna repair]]
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[[Category: Oxidoreductase/dna complex]]
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[[Category: Oxidoreductase-dna complex]]
[[Category: Protein dna interaction]]
[[Category: Protein dna interaction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 10:13:18 2008''
 

Current revision

X-ray structure of E coli AlkB crosslinked to dsDNA in the active site

PDB ID 3bkz

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