1diz

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(New page: 200px<br /><applet load="1diz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1diz, resolution 2.50&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1diz.gif|left|200px]]<br /><applet load="1diz" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1diz, resolution 2.50&Aring;" />
 
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'''CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA==
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The Escherichia coli AlkA protein is a base excision repair glycosylase, that removes a variety of alkylated bases from DNA. The 2.5 A crystal, structure of AlkA complexed to DNA shows a large distortion in the bound, DNA. The enzyme flips a 1-azaribose abasic nucleotide out of DNA and, induces a 66 degrees bend in the DNA with a marked widening of the minor, groove. The position of the 1-azaribose in the enzyme active site suggests, an S(N)1-type mechanism for the glycosylase reaction, in which the, essential catalytic Asp238 provides direct assistance for base removal., Catalytic selectivity might result from the enhanced stacking of, positively charged, alkylated bases against the aromatic side chain of, Trp272 in conjunction with the relative ease of cleaving the weakened, glycosylic bond of these modified nucleotides. The structure of the, AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH), glycosylase complexed to DNA. Modeling studies suggest that other HhH, glycosylases can bind to DNA in a similar manner.
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<StructureSection load='1diz' size='340' side='right'caption='[[1diz]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1diz]] is a 6 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=1DIZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DIZ FirstGlance]. <br>
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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]] 2.5&#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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NRI:PHOSPHORIC+ACID+MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)+ESTER'>NRI</scene></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=1diz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1diz OCA], [https://pdbe.org/1diz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1diz RCSB], [https://www.ebi.ac.uk/pdbsum/1diz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1diz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/3MG2_ECOLI 3MG2_ECOLI] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine, 3-methylguanine, 7-methylguanine, O2-methylthymine, and O2-methylcytosine 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/di/1diz_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=1diz ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1DIZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DIZ OCA].
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA., Hollis T, Ichikawa Y, Ellenberger T, EMBO J. 2000 Feb 15;19(4):758-66. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10675345 10675345]
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[[Category: DNA-3-methyladenine glycosylase II]]
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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: Ellenberger, T.E.]]
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[[Category: Ellenberger TE]]
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[[Category: Hollis, T.]]
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[[Category: Hollis T]]
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[[Category: Ichikawa, Y.]]
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[[Category: Ichikawa Y]]
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[[Category: NA]]
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[[Category: 1-azaribose]]
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[[Category: 3-methyladenine dna glycosylase]]
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[[Category: alka]]
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[[Category: helix-hairpin-helix]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:19:01 2007''
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Current revision

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

PDB ID 1diz

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