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==Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD==
==Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD==
<StructureSection load='3bvs' size='340' side='right' caption='[[3bvs]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='3bvs' size='340' side='right'caption='[[3bvs]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3bvs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BVS FirstGlance]. <br>
<table><tr><td colspan='2'>[[3bvs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_10987 Bacillus cereus ATCC 10987]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BVS FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AlkD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1396 Bacillus cereus])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bvs RCSB], [http://www.ebi.ac.uk/pdbsum/3bvs PDBsum]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvs OCA], [https://pdbe.org/3bvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bvs RCSB], [https://www.ebi.ac.uk/pdbsum/3bvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvs ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q816E8_BACCR Q816E8_BACCR]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/3bvs_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/3bvs_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=3bvs ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA glycosylases safeguard the genome by locating and excising chemically modified bases from DNA. AlkD is a recently discovered bacterial DNA glycosylase that removes positively charged methylpurines from DNA, and was predicted to adopt a protein fold distinct from from those of other DNA repair proteins. The crystal structure of Bacillus cereus AlkD presented here shows that the protein is composed exclusively of helical HEAT-like repeats, which form a solenoid perfectly shaped to accommodate a DNA duplex on the concave surface. Structural analysis of the variant HEAT repeats in AlkD provides a rationale for how this protein scaffolding motif has been modified to bind DNA. We report 7mG excision and DNA binding activities of AlkD mutants, along with a comparison of alkylpurine DNA glycosylase structures. Together, these data provide important insight into the requirements for alkylation repair within DNA and suggest that AlkD utilizes a novel strategy to manipulate DNA in its search for alkylpurine bases.
A new protein architecture for processing alkylation damaged DNA: the crystal structure of DNA glycosylase AlkD.,Rubinson EH, Metz AH, O'Quin J, Eichman BF J Mol Biol. 2008 Aug 1;381(1):13-23. Epub 2008 Jun 5. PMID:18585735<ref>PMID:18585735</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[DNA glycosylase|DNA glycosylase]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus cereus]]
[[Category: Bacillus cereus ATCC 10987]]
[[Category: Eichman, B F.]]
[[Category: Large Structures]]
[[Category: Rubinson, E H.]]
[[Category: Eichman BF]]
[[Category: Alkylpurine]]
[[Category: Rubinson EH]]
[[Category: Dna glycosylase]]
[[Category: Dna repair]]
[[Category: Heat repeat]]
[[Category: Hydrolase]]

Latest revision as of 09:31, 21 February 2024

Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD

3bvs, resolution 2.10Å

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