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1vrl

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(New page: 200px<br /><applet load="1vrl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vrl, resolution 2.50&Aring;" /> '''MutY adenine glycosy...)
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[[Image:1vrl.gif|left|200px]]<br /><applet load="1vrl" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1vrl, resolution 2.50&Aring;" />
 
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'''MutY adenine glycosylase in complex with DNA and soaked adenine free base'''<br />
 
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==Overview==
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==MutY adenine glycosylase in complex with DNA and soaked adenine free base==
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The genomes of aerobic organisms suffer chronic oxidation of guanine to, the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases, misread oxoG residues and insert adenine instead of cytosine opposite the, oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic, lesions, and both must undergo base-specific replacement to restore the, original C*G pair. Doing so represents a formidable challenge to the DNA, repair machinery, because adenine makes up roughly 25% of the bases in, most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase, (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to, C*G by removing the inappropriately paired adenine base from the DNA, backbone. A central issue concerning MutY function is the mechanism by, which A*oxoG mispairs are targeted among the vast excess of A*T pairs., Here we report the use of disulphide crosslinking to obtain, high-resolution crystal structures of MutY-DNA lesion-recognition, complexes. These structures reveal the basis for recognizing both lesions, in the A*oxoG pair and for catalysing removal of the adenine base.
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<StructureSection load='1vrl' size='340' side='right'caption='[[1vrl]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1vrl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rrt 1rrt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VRL 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=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1vrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vrl OCA], [https://pdbe.org/1vrl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vrl RCSB], [https://www.ebi.ac.uk/pdbsum/1vrl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vrl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MUTY_GEOSE MUTY_GEOSE] Base excision repair (BER) glycosylase that initiates repair of A:oxoG to C:G by removing the inappropriately paired adenine base from the DNA backbone, generating an abasic site product (PubMed:25995449) (PubMed:14961129). 8-oxoguanine (oxoG) is a genotoxic DNA lesion resulting from oxidation of guanine; this residue is misread by replicative DNA polymerases, that insert adenine instead of cytosine opposite the oxidized damaged base. Shows a powerful dicrimination of A versus C, since it does not cleave cytosine in oxoG:C pairs (PubMed:25995449). May also be able to remove adenine from A:G mispairs, although this activity may not be physiologically relevant (PubMed:14961129).<ref>PMID:25995449</ref> <ref>PMID:14961129</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/vr/1vrl_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=1vrl 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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The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic lesions, and both must undergo base-specific replacement to restore the original C*G pair. Doing so represents a formidable challenge to the DNA repair machinery, because adenine makes up roughly 25% of the bases in most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to C*G by removing the inappropriately paired adenine base from the DNA backbone. A central issue concerning MutY function is the mechanism by which A*oxoG mispairs are targeted among the vast excess of A*T pairs. Here we report the use of disulphide crosslinking to obtain high-resolution crystal structures of MutY-DNA lesion-recognition complexes. These structures reveal the basis for recognizing both lesions in the A*oxoG pair and for catalysing removal of the adenine base.
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==About this Structure==
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Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase.,Fromme JC, Banerjee A, Huang SJ, Verdine GL Nature. 2004 Feb 12;427(6975):652-6. PMID:14961129<ref>PMID:14961129</ref>
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1VRL is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with CA, SF4 and ADE as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1RRT. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VRL OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase., Fromme JC, Banerjee A, Huang SJ, Verdine GL, Nature. 2004 Feb 12;427(6975):652-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14961129 14961129]
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</div>
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[[Category: Geobacillus stearothermophilus]]
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<div class="pdbe-citations 1vrl" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Banerjee, A.]]
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[[Category: Fromme, J.C.]]
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[[Category: Huang, S.J.]]
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[[Category: Verdine, G.L.]]
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[[Category: ADE]]
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[[Category: CA]]
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[[Category: SF4]]
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[[Category: 8-oxoguanine]]
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[[Category: dna glycosylase]]
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[[Category: dna repair]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:06:11 2007''
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==See Also==
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Geobacillus stearothermophilus]]
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[[Category: Large Structures]]
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[[Category: Banerjee A]]
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[[Category: Fromme JC]]
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[[Category: Huang SJ]]
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[[Category: Verdine GL]]

Current revision

MutY adenine glycosylase in complex with DNA and soaked adenine free base

PDB ID 1vrl

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